diff --git a/api/db/indexSync.js b/api/db/indexSync.js
index c86598d108..b39f018b3a 100644
--- a/api/db/indexSync.js
+++ b/api/db/indexSync.js
@@ -4,6 +4,7 @@ const { logger } = require('@librechat/data-schemas');
 const { CacheKeys } = require('librechat-data-provider');
 const { isEnabled, FlowStateManager } = require('@librechat/api');
 const { getLogStores } = require('~/cache');
+const { batchResetMeiliFlags } = require('./utils');
 
 const Conversation = mongoose.models.Conversation;
 const Message = mongoose.models.Message;
@@ -189,6 +190,11 @@ async function ensureFilterableAttributes(client) {
  */
 async function performSync(flowManager, flowId, flowType) {
   try {
+    if (indexingDisabled === true) {
+      logger.info('[indexSync] Indexing is disabled, skipping...');
+      return { messagesSync: false, convosSync: false };
+    }
+
     const client = MeiliSearchClient.getInstance();
 
     const { status } = await client.health();
@@ -196,11 +202,6 @@ async function performSync(flowManager, flowId, flowType) {
       throw new Error('Meilisearch not available');
     }
 
-    if (indexingDisabled === true) {
-      logger.info('[indexSync] Indexing is disabled, skipping...');
-      return { messagesSync: false, convosSync: false };
-    }
-
     /** Ensures indexes have proper filterable attributes configured */
     const { settingsUpdated, orphanedDocsFound: _orphanedDocsFound } =
       await ensureFilterableAttributes(client);
@@ -215,11 +216,8 @@ async function performSync(flowManager, flowId, flowType) {
       );
 
       // Reset sync flags to force full re-sync
-      await Message.collection.updateMany({ _meiliIndex: true }, { $set: { _meiliIndex: false } });
-      await Conversation.collection.updateMany(
-        { _meiliIndex: true },
-        { $set: { _meiliIndex: false } },
-      );
+      await batchResetMeiliFlags(Message.collection);
+      await batchResetMeiliFlags(Conversation.collection);
     }
 
     // Check if we need to sync messages
diff --git a/api/db/utils.js b/api/db/utils.js
new file mode 100644
index 0000000000..4a311d9832
--- /dev/null
+++ b/api/db/utils.js
@@ -0,0 +1,90 @@
+const { logger } = require('@librechat/data-schemas');
+
+const sleep = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
+
+/**
+ * Batch update documents in chunks to avoid timeouts on weak instances
+ * @param {mongoose.Collection} collection - MongoDB collection
+ * @returns {Promise<number>} - Total modified count
+ * @throws {Error} - Throws if database operations fail (e.g., network issues, connection loss, permission problems)
+ */
+async function batchResetMeiliFlags(collection) {
+  const DEFAULT_BATCH_SIZE = 1000;
+
+  let BATCH_SIZE = parseEnvInt('MEILI_SYNC_BATCH_SIZE', DEFAULT_BATCH_SIZE);
+  if (BATCH_SIZE === 0) {
+    logger.warn(
+      `[batchResetMeiliFlags] MEILI_SYNC_BATCH_SIZE cannot be 0. Using default: ${DEFAULT_BATCH_SIZE}`,
+    );
+    BATCH_SIZE = DEFAULT_BATCH_SIZE;
+  }
+
+  const BATCH_DELAY_MS = parseEnvInt('MEILI_SYNC_DELAY_MS', 100);
+  let totalModified = 0;
+  let hasMore = true;
+
+  try {
+    while (hasMore) {
+      const docs = await collection
+        .find({ expiredAt: null, _meiliIndex: true }, { projection: { _id: 1 } })
+        .limit(BATCH_SIZE)
+        .toArray();
+
+      if (docs.length === 0) {
+        break;
+      }
+
+      const ids = docs.map((doc) => doc._id);
+      const result = await collection.updateMany(
+        { _id: { $in: ids } },
+        { $set: { _meiliIndex: false } },
+      );
+
+      totalModified += result.modifiedCount;
+      process.stdout.write(
+        `\r  Updating ${collection.collectionName}: ${totalModified} documents...`,
+      );
+
+      if (docs.length < BATCH_SIZE) {
+        hasMore = false;
+      }
+
+      if (hasMore && BATCH_DELAY_MS > 0) {
+        await sleep(BATCH_DELAY_MS);
+      }
+    }
+
+    return totalModified;
+  } catch (error) {
+    throw new Error(
+      `Failed to batch reset Meili flags for collection '${collection.collectionName}' after processing ${totalModified} documents: ${error.message}`,
+    );
+  }
+}
+
+/**
+ * Parse and validate an environment variable as a positive integer
+ * @param {string} varName - Environment variable name
+ * @param {number} defaultValue - Default value to use if invalid or missing
+ * @returns {number} - Parsed value or default
+ */
+function parseEnvInt(varName, defaultValue) {
+  const value = process.env[varName];
+  if (!value) {
+    return defaultValue;
+  }
+
+  const parsed = parseInt(value, 10);
+  if (isNaN(parsed) || parsed < 0) {
+    logger.warn(
+      `[batchResetMeiliFlags] Invalid value for ${varName}="${value}". Expected a positive integer. Using default: ${defaultValue}`,
+    );
+    return defaultValue;
+  }
+
+  return parsed;
+}
+
+module.exports = {
+  batchResetMeiliFlags,
+};
diff --git a/api/db/utils.spec.js b/api/db/utils.spec.js
new file mode 100644
index 0000000000..8b32b4aea8
--- /dev/null
+++ b/api/db/utils.spec.js
@@ -0,0 +1,521 @@
+const mongoose = require('mongoose');
+const { MongoMemoryServer } = require('mongodb-memory-server');
+const { batchResetMeiliFlags } = require('./utils');
+
+describe('batchResetMeiliFlags', () => {
+  let mongoServer;
+  let testCollection;
+  const ORIGINAL_BATCH_SIZE = process.env.MEILI_SYNC_BATCH_SIZE;
+  const ORIGINAL_BATCH_DELAY = process.env.MEILI_SYNC_DELAY_MS;
+
+  beforeAll(async () => {
+    mongoServer = await MongoMemoryServer.create();
+    const mongoUri = mongoServer.getUri();
+    await mongoose.connect(mongoUri);
+  });
+
+  afterAll(async () => {
+    await mongoose.disconnect();
+    await mongoServer.stop();
+
+    // Restore original env variables
+    if (ORIGINAL_BATCH_SIZE !== undefined) {
+      process.env.MEILI_SYNC_BATCH_SIZE = ORIGINAL_BATCH_SIZE;
+    } else {
+      delete process.env.MEILI_SYNC_BATCH_SIZE;
+    }
+
+    if (ORIGINAL_BATCH_DELAY !== undefined) {
+      process.env.MEILI_SYNC_DELAY_MS = ORIGINAL_BATCH_DELAY;
+    } else {
+      delete process.env.MEILI_SYNC_DELAY_MS;
+    }
+  });
+
+  beforeEach(async () => {
+    // Create a fresh collection for each test
+    testCollection = mongoose.connection.db.collection('test_meili_batch');
+    await testCollection.deleteMany({});
+
+    // Reset env variables to defaults
+    delete process.env.MEILI_SYNC_BATCH_SIZE;
+    delete process.env.MEILI_SYNC_DELAY_MS;
+  });
+
+  afterEach(async () => {
+    if (testCollection) {
+      await testCollection.deleteMany({});
+    }
+  });
+
+  describe('basic functionality', () => {
+    it('should reset _meiliIndex flag for documents with expiredAt: null and _meiliIndex: true', async () => {
+      // Insert test documents
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true, name: 'doc1' },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true, name: 'doc2' },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true, name: 'doc3' },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(3);
+
+      const updatedDocs = await testCollection.find({ _meiliIndex: false }).toArray();
+      expect(updatedDocs).toHaveLength(3);
+
+      const notUpdatedDocs = await testCollection.find({ _meiliIndex: true }).toArray();
+      expect(notUpdatedDocs).toHaveLength(0);
+    });
+
+    it('should not modify documents with expiredAt set', async () => {
+      const expiredDate = new Date();
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: expiredDate, _meiliIndex: true },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+
+      const expiredDoc = await testCollection.findOne({ expiredAt: expiredDate });
+      expect(expiredDoc._meiliIndex).toBe(true);
+    });
+
+    it('should not modify documents with _meiliIndex: false', async () => {
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: false },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+    });
+
+    it('should return 0 when no documents match the criteria', async () => {
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: new Date(), _meiliIndex: true },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: false },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(0);
+    });
+
+    it('should return 0 when collection is empty', async () => {
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(0);
+    });
+  });
+
+  describe('batch processing', () => {
+    it('should process documents in batches according to MEILI_SYNC_BATCH_SIZE', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = '2';
+
+      const docs = [];
+      for (let i = 0; i < 5; i++) {
+        docs.push({
+          _id: new mongoose.Types.ObjectId(),
+          expiredAt: null,
+          _meiliIndex: true,
+          name: `doc${i}`,
+        });
+      }
+      await testCollection.insertMany(docs);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(5);
+
+      const updatedDocs = await testCollection.find({ _meiliIndex: false }).toArray();
+      expect(updatedDocs).toHaveLength(5);
+    });
+
+    it('should handle large datasets with small batch sizes', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = '10';
+
+      const docs = [];
+      for (let i = 0; i < 25; i++) {
+        docs.push({
+          _id: new mongoose.Types.ObjectId(),
+          expiredAt: null,
+          _meiliIndex: true,
+        });
+      }
+      await testCollection.insertMany(docs);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(25);
+    });
+
+    it('should use default batch size of 1000 when env variable is not set', async () => {
+      // Create exactly 1000 documents to verify default batch behavior
+      const docs = [];
+      for (let i = 0; i < 1000; i++) {
+        docs.push({
+          _id: new mongoose.Types.ObjectId(),
+          expiredAt: null,
+          _meiliIndex: true,
+        });
+      }
+      await testCollection.insertMany(docs);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1000);
+    });
+  });
+
+  describe('return value', () => {
+    it('should return correct modified count', async () => {
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      await expect(batchResetMeiliFlags(testCollection)).resolves.toBe(1);
+    });
+  });
+
+  describe('batch delay', () => {
+    it('should respect MEILI_SYNC_DELAY_MS between batches', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = '2';
+      process.env.MEILI_SYNC_DELAY_MS = '50';
+
+      const docs = [];
+      for (let i = 0; i < 5; i++) {
+        docs.push({
+          _id: new mongoose.Types.ObjectId(),
+          expiredAt: null,
+          _meiliIndex: true,
+        });
+      }
+      await testCollection.insertMany(docs);
+
+      const startTime = Date.now();
+      await batchResetMeiliFlags(testCollection);
+      const endTime = Date.now();
+
+      // With 5 documents and batch size 2, we need 3 batches
+      // That means 2 delays between batches (not after the last one)
+      // So minimum time should be around 100ms (2 * 50ms)
+      // Using a slightly lower threshold to account for timing variations
+      const elapsed = endTime - startTime;
+      expect(elapsed).toBeGreaterThanOrEqual(80);
+    });
+
+    it('should not delay when MEILI_SYNC_DELAY_MS is 0', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = '2';
+      process.env.MEILI_SYNC_DELAY_MS = '0';
+
+      const docs = [];
+      for (let i = 0; i < 5; i++) {
+        docs.push({
+          _id: new mongoose.Types.ObjectId(),
+          expiredAt: null,
+          _meiliIndex: true,
+        });
+      }
+      await testCollection.insertMany(docs);
+
+      const startTime = Date.now();
+      await batchResetMeiliFlags(testCollection);
+      const endTime = Date.now();
+
+      const elapsed = endTime - startTime;
+      // Should complete without intentional delays, but database operations still take time
+      // Just verify it completes and returns the correct count
+      expect(elapsed).toBeLessThan(1000); // More reasonable upper bound
+
+      const result = await testCollection.countDocuments({ _meiliIndex: false });
+      expect(result).toBe(5);
+    });
+
+    it('should not delay after the last batch', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = '3';
+      process.env.MEILI_SYNC_DELAY_MS = '100';
+
+      // Exactly 3 documents - should fit in one batch, no delay
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      // Verify all 3 documents were processed in a single batch
+      expect(result).toBe(3);
+
+      const updatedDocs = await testCollection.countDocuments({ _meiliIndex: false });
+      expect(updatedDocs).toBe(3);
+    });
+  });
+
+  describe('edge cases', () => {
+    it('should handle documents without _meiliIndex field', async () => {
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      // Only one document has _meiliIndex: true
+      expect(result).toBe(1);
+    });
+
+    it('should handle mixed document states correctly', async () => {
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: false },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: new Date(), _meiliIndex: true },
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(2);
+
+      const flaggedDocs = await testCollection
+        .find({ expiredAt: null, _meiliIndex: false })
+        .toArray();
+      expect(flaggedDocs).toHaveLength(3); // 2 were updated, 1 was already false
+    });
+  });
+
+  describe('error handling', () => {
+    it('should throw error with context when find operation fails', async () => {
+      const mockCollection = {
+        collectionName: 'test_meili_batch',
+        find: jest.fn().mockReturnValue({
+          limit: jest.fn().mockReturnValue({
+            toArray: jest.fn().mockRejectedValue(new Error('Network error')),
+          }),
+        }),
+      };
+
+      await expect(batchResetMeiliFlags(mockCollection)).rejects.toThrow(
+        "Failed to batch reset Meili flags for collection 'test_meili_batch' after processing 0 documents: Network error",
+      );
+    });
+
+    it('should throw error with context when updateMany operation fails', async () => {
+      const mockCollection = {
+        collectionName: 'test_meili_batch',
+        find: jest.fn().mockReturnValue({
+          limit: jest.fn().mockReturnValue({
+            toArray: jest
+              .fn()
+              .mockResolvedValue([
+                { _id: new mongoose.Types.ObjectId() },
+                { _id: new mongoose.Types.ObjectId() },
+              ]),
+          }),
+        }),
+        updateMany: jest.fn().mockRejectedValue(new Error('Connection lost')),
+      };
+
+      await expect(batchResetMeiliFlags(mockCollection)).rejects.toThrow(
+        "Failed to batch reset Meili flags for collection 'test_meili_batch' after processing 0 documents: Connection lost",
+      );
+    });
+
+    it('should include documents processed count in error when failure occurs mid-batch', async () => {
+      // Set batch size to 2 to force multiple batches
+      process.env.MEILI_SYNC_BATCH_SIZE = '2';
+      process.env.MEILI_SYNC_DELAY_MS = '0'; // No delay for faster test
+
+      let findCallCount = 0;
+      let updateCallCount = 0;
+
+      const mockCollection = {
+        collectionName: 'test_meili_batch',
+        find: jest.fn().mockReturnValue({
+          limit: jest.fn().mockReturnValue({
+            toArray: jest.fn().mockImplementation(() => {
+              findCallCount++;
+              // Return 2 documents for first two calls (to keep loop going)
+              // Return 2 documents for third call (to trigger third update which will fail)
+              if (findCallCount <= 3) {
+                return Promise.resolve([
+                  { _id: new mongoose.Types.ObjectId() },
+                  { _id: new mongoose.Types.ObjectId() },
+                ]);
+              }
+              // Should not reach here due to error
+              return Promise.resolve([]);
+            }),
+          }),
+        }),
+        updateMany: jest.fn().mockImplementation(() => {
+          updateCallCount++;
+          if (updateCallCount === 1) {
+            return Promise.resolve({ modifiedCount: 2 });
+          } else if (updateCallCount === 2) {
+            return Promise.resolve({ modifiedCount: 2 });
+          } else {
+            return Promise.reject(new Error('Database timeout'));
+          }
+        }),
+      };
+
+      await expect(batchResetMeiliFlags(mockCollection)).rejects.toThrow(
+        "Failed to batch reset Meili flags for collection 'test_meili_batch' after processing 4 documents: Database timeout",
+      );
+    });
+
+    it('should use collection.collectionName in error messages', async () => {
+      const mockCollection = {
+        collectionName: 'messages',
+        find: jest.fn().mockReturnValue({
+          limit: jest.fn().mockReturnValue({
+            toArray: jest.fn().mockRejectedValue(new Error('Permission denied')),
+          }),
+        }),
+      };
+
+      await expect(batchResetMeiliFlags(mockCollection)).rejects.toThrow(
+        "Failed to batch reset Meili flags for collection 'messages' after processing 0 documents: Permission denied",
+      );
+    });
+  });
+
+  describe('environment variable validation', () => {
+    let warnSpy;
+
+    beforeEach(() => {
+      // Mock logger.warn to track warning calls
+      const { logger } = require('@librechat/data-schemas');
+      warnSpy = jest.spyOn(logger, 'warn').mockImplementation(() => {});
+    });
+
+    afterEach(() => {
+      if (warnSpy) {
+        warnSpy.mockRestore();
+      }
+    });
+
+    it('should log warning and use default when MEILI_SYNC_BATCH_SIZE is not a number', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = 'abc';
+
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+      expect(warnSpy).toHaveBeenCalledWith(
+        expect.stringContaining('Invalid value for MEILI_SYNC_BATCH_SIZE="abc"'),
+      );
+      expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining('Using default: 1000'));
+    });
+
+    it('should log warning and use default when MEILI_SYNC_DELAY_MS is not a number', async () => {
+      process.env.MEILI_SYNC_DELAY_MS = 'xyz';
+
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+      expect(warnSpy).toHaveBeenCalledWith(
+        expect.stringContaining('Invalid value for MEILI_SYNC_DELAY_MS="xyz"'),
+      );
+      expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining('Using default: 100'));
+    });
+
+    it('should log warning and use default when MEILI_SYNC_BATCH_SIZE is negative', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = '-50';
+
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+      expect(warnSpy).toHaveBeenCalledWith(
+        expect.stringContaining('Invalid value for MEILI_SYNC_BATCH_SIZE="-50"'),
+      );
+    });
+
+    it('should log warning and use default when MEILI_SYNC_DELAY_MS is negative', async () => {
+      process.env.MEILI_SYNC_DELAY_MS = '-100';
+
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+      expect(warnSpy).toHaveBeenCalledWith(
+        expect.stringContaining('Invalid value for MEILI_SYNC_DELAY_MS="-100"'),
+      );
+    });
+
+    it('should accept valid positive integer values without warnings', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = '500';
+      process.env.MEILI_SYNC_DELAY_MS = '50';
+
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+      expect(warnSpy).not.toHaveBeenCalled();
+    });
+
+    it('should log warning and use default when MEILI_SYNC_BATCH_SIZE is zero', async () => {
+      process.env.MEILI_SYNC_BATCH_SIZE = '0';
+
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+      expect(warnSpy).toHaveBeenCalledWith(
+        expect.stringContaining('MEILI_SYNC_BATCH_SIZE cannot be 0. Using default: 1000'),
+      );
+    });
+
+    it('should accept zero as a valid value for MEILI_SYNC_DELAY_MS without warnings', async () => {
+      process.env.MEILI_SYNC_DELAY_MS = '0';
+
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+      expect(warnSpy).not.toHaveBeenCalled();
+    });
+
+    it('should not log warnings when environment variables are not set', async () => {
+      delete process.env.MEILI_SYNC_BATCH_SIZE;
+      delete process.env.MEILI_SYNC_DELAY_MS;
+
+      await testCollection.insertMany([
+        { _id: new mongoose.Types.ObjectId(), expiredAt: null, _meiliIndex: true },
+      ]);
+
+      const result = await batchResetMeiliFlags(testCollection);
+
+      expect(result).toBe(1);
+      expect(warnSpy).not.toHaveBeenCalled();
+    });
+  });
+});
diff --git a/config/reset-meili-sync.js b/config/reset-meili-sync.js
index c07a0ac32d..60f45246a8 100644
--- a/config/reset-meili-sync.js
+++ b/config/reset-meili-sync.js
@@ -1,8 +1,10 @@
 const path = require('path');
 const mongoose = require('mongoose');
 require('module-alias')({ base: path.resolve(__dirname, '..', 'api') });
+require('dotenv').config({ path: path.resolve(__dirname, '..', '.env') });
 const { askQuestion, silentExit } = require('./helpers');
 const connect = require('./connect');
+const { batchResetMeiliFlags } = require('~/db/utils');
 
 (async () => {
   await connect();
@@ -24,32 +26,39 @@ const connect = require('./connect');
   }
 
   try {
+    const clearProgress = () => process.stdout.write('\r' + ' '.repeat(70) + '\r');
+
     // Reset _meiliIndex flags for messages
     console.cyan('\nResetting message sync flags...');
-    const messageResult = await mongoose.connection.db
-      .collection('messages')
-      .updateMany({ _meiliIndex: true }, { $set: { _meiliIndex: false } });
-
-    console.green(`✓ Reset ${messageResult.modifiedCount} message sync flags`);
+    const messages = mongoose.connection.db.collection('messages');
+    const messageModifiedCount = await batchResetMeiliFlags(messages);
+    clearProgress();
+    console.green(`✓ Reset ${messageModifiedCount} message sync flags`);
 
     // Reset _meiliIndex flags for conversations
     console.cyan('\nResetting conversation sync flags...');
-    const conversationResult = await mongoose.connection.db
-      .collection('conversations')
-      .updateMany({ _meiliIndex: true }, { $set: { _meiliIndex: false } });
+    const conversationsCollection = mongoose.connection.db.collection('conversations');
+    const conversationModifiedCount = await batchResetMeiliFlags(conversationsCollection);
+    clearProgress();
+    console.green(`✓ Reset ${conversationModifiedCount} conversation sync flags`);
 
-    console.green(`✓ Reset ${conversationResult.modifiedCount} conversation sync flags`);
+    // Query to count only non-expired documents that are queued for sync (_meiliIndex: false)
+    // This represents documents that need to be indexed, not the total collection size
+    const queryTotal = { expiredAt: null, _meiliIndex: false };
 
-    // Get current counts
-    const totalMessages = await mongoose.connection.db.collection('messages').countDocuments();
+    // Get current counts of documents queued for sync
+    const totalMessages = await mongoose.connection.db
+      .collection('messages')
+      .countDocuments(queryTotal);
     const totalConversations = await mongoose.connection.db
       .collection('conversations')
-      .countDocuments();
+      .countDocuments(queryTotal);
 
     console.purple('\n---------------------------------------');
     console.green('MeiliSearch sync flags have been reset successfully!');
-    console.cyan(`\nTotal messages to sync: ${totalMessages}`);
-    console.cyan(`Total conversations to sync: ${totalConversations}`);
+    console.cyan(`\nDocuments queued for sync:`);
+    console.cyan(`Messages: ${totalMessages}`);
+    console.cyan(`Conversations: ${totalConversations}`);
     console.yellow('\nThe next time LibreChat starts or performs a sync check,');
     console.yellow('all data will be re-indexed into MeiliSearch.');
     console.purple('---------------------------------------\n');
diff --git a/packages/data-schemas/src/schema/convo.ts b/packages/data-schemas/src/schema/convo.ts
index 2933f2e95b..e6a9ede6be 100644
--- a/packages/data-schemas/src/schema/convo.ts
+++ b/packages/data-schemas/src/schema/convo.ts
@@ -45,4 +45,7 @@ convoSchema.index({ expiredAt: 1 }, { expireAfterSeconds: 0 });
 convoSchema.index({ createdAt: 1, updatedAt: 1 });
 convoSchema.index({ conversationId: 1, user: 1 }, { unique: true });
 
+// index for MeiliSearch sync operations
+convoSchema.index({ _meiliIndex: 1, expiredAt: 1 });
+
 export default convoSchema;
diff --git a/packages/data-schemas/src/schema/message.ts b/packages/data-schemas/src/schema/message.ts
index 5dece654d7..8bfdb1b39e 100644
--- a/packages/data-schemas/src/schema/message.ts
+++ b/packages/data-schemas/src/schema/message.ts
@@ -148,4 +148,7 @@ messageSchema.index({ expiredAt: 1 }, { expireAfterSeconds: 0 });
 messageSchema.index({ createdAt: 1 });
 messageSchema.index({ messageId: 1, user: 1 }, { unique: true });
 
+// index for MeiliSearch sync operations
+messageSchema.index({ _meiliIndex: 1, expiredAt: 1 });
+
 export default messageSchema;