diff --git a/client/src/components/Prompts/PromptForm.tsx b/client/src/components/Prompts/PromptForm.tsx
index c3c87f642c..9a760dbd7d 100644
--- a/client/src/components/Prompts/PromptForm.tsx
+++ b/client/src/components/Prompts/PromptForm.tsx
@@ -11,6 +11,7 @@ import {
   ResourceType,
   PermissionBits,
   PermissionTypes,
+  EToolResources,
 } from 'librechat-data-provider';
 import type { TCreatePrompt, TPrompt, TPromptGroup } from 'librechat-data-provider';
 import {
@@ -193,16 +194,18 @@ const PromptForm = () => {
     handleFileRemove,
     setFiles,
   } = usePromptFileHandling({
-    onFileChange: () => {
+    onFileChange: (updatedFiles) => {
       // Auto-save when files are added/removed
-      console.log('onFileChange called', { canEdit, selectedPrompt: !!selectedPrompt });
+      console.log('onFileChange called', {
+        canEdit,
+        selectedPrompt: !!selectedPrompt,
+        updatedFiles,
+      });
       if (canEdit && selectedPrompt) {
         const currentPromptText = getValues('prompt');
-        console.log('Calling onSave with:', currentPromptText);
-        // Use setTimeout to ensure file state is updated before calling onSave
-        setTimeout(() => {
-          onSave(currentPromptText);
-        }, 100);
+        console.log('Calling onSave with:', currentPromptText, 'and updated files:', updatedFiles);
+        // Call onSave with the updated files to ensure correct tool_resources
+        onSave(currentPromptText, updatedFiles);
       }
     },
   });
@@ -280,8 +283,33 @@ const PromptForm = () => {
     },
   });
 
+  // Helper function to get tool resources from a specific files array
+  const getToolResourcesFromFiles = useCallback((files: ExtendedFile[]) => {
+    if (files.length === 0) {
+      return undefined;
+    }
+
+    const toolResources: AgentToolResources = {};
+
+    files.forEach((file) => {
+      if (!file.file_id) return; // Skip files that haven't been uploaded yet
+
+      // Initialize the tool resource if it doesn't exist
+      if (!toolResources[file.tool_resource]) {
+        toolResources[file.tool_resource] = { file_ids: [] };
+      }
+
+      // Add file_id to the appropriate tool resource
+      if (!toolResources[file.tool_resource]!.file_ids!.includes(file.file_id)) {
+        toolResources[file.tool_resource]!.file_ids!.push(file.file_id);
+      }
+    });
+
+    return Object.keys(toolResources).length > 0 ? toolResources : undefined;
+  }, []);
+
   const onSave = useCallback(
-    (value: string) => {
+    (value: string, updatedFiles?: ExtendedFile[]) => {
       if (!canEdit) {
         return;
       }
@@ -299,7 +327,10 @@ const PromptForm = () => {
         return;
       }
 
-      const toolResources = getToolResources();
+      // Use updated files if provided, otherwise use current hook state
+      const toolResources = updatedFiles
+        ? getToolResourcesFromFiles(updatedFiles)
+        : getToolResources();
       const tempPrompt: TCreatePrompt = {
         prompt: {
           type: selectedPrompt.type ?? 'text',
diff --git a/client/src/hooks/Prompts/usePromptFileHandling.ts b/client/src/hooks/Prompts/usePromptFileHandling.ts
index d88340b00f..2b6eaf56ac 100644
--- a/client/src/hooks/Prompts/usePromptFileHandling.ts
+++ b/client/src/hooks/Prompts/usePromptFileHandling.ts
@@ -4,14 +4,14 @@ import { useToastContext } from '@librechat/client';
 import { EModelEndpoint, EToolResources, FileSources } from 'librechat-data-provider';
 import type { AgentToolResources, TFile } from 'librechat-data-provider';
 import type { ExtendedFile } from '~/common';
-import { useUploadFileMutation, useGetFiles, useDeleteFilesMutation } from '~/data-provider';
+import { useUploadFileMutation, useGetFiles } from '~/data-provider';
 import { useAuthContext } from '~/hooks';
 import { logger } from '~/utils';
 
 interface UsePromptFileHandling {
   fileSetter?: (files: ExtendedFile[]) => void;
   initialFiles?: ExtendedFile[];
-  onFileChange?: () => void; // Callback when files are added/removed
+  onFileChange?: (updatedFiles: ExtendedFile[]) => void; // Callback when files are added/removed
 }
 
 /**
@@ -38,16 +38,6 @@ export const usePromptFileHandling = (params?: UsePromptFileHandling) => {
   const [filesLoading, setFilesLoading] = useState(false);
   const abortControllerRef = useRef<AbortController | null>(null);
 
-  const deleteFileMutation = useDeleteFilesMutation({
-    onSuccess: () => {
-      params?.onFileChange?.();
-    },
-    onError: (error) => {
-      logger.error('Error deleting file:', error);
-      params?.onFileChange?.();
-    },
-  });
-
   const uploadFile = useUploadFileMutation({
     onSuccess: (data) => {
       logger.log('File uploaded successfully', data);
@@ -80,8 +70,27 @@ export const usePromptFileHandling = (params?: UsePromptFileHandling) => {
         status: 'success',
       });
 
-      // Call the onFileChange callback to trigger save
-      params?.onFileChange?.();
+      // Call the onFileChange callback to trigger save with updated files
+      const updatedFiles = files.map((file) => {
+        if (file.temp_file_id === data.temp_file_id) {
+          return {
+            ...file,
+            file_id: data.file_id,
+            filepath: data.filepath,
+            progress: 1,
+            attached: true,
+            preview: data.filepath || file.preview,
+            filename: data.filename || file.filename,
+            type: data.type || file.type,
+            size: data.bytes || file.size,
+            width: data.width || file.width,
+            height: data.height || file.height,
+            source: data.source || file.source,
+          };
+        }
+        return file;
+      });
+      params?.onFileChange?.(updatedFiles);
     },
     onError: (error, body) => {
       logger.error('File upload error:', error);
@@ -228,8 +237,8 @@ export const usePromptFileHandling = (params?: UsePromptFileHandling) => {
   // Handle file removal
   const handleFileRemove = useCallback(
     (fileId: string) => {
-      // Call delete API to remove from database
-      deleteFileMutation.mutate([fileId]);
+      // For prompts, we only remove the file from the current prompt's tool_resources
+      // We don't delete the file from the database to preserve previous versions
 
       setFiles((prev) => {
         return prev.filter((file) => {
@@ -243,8 +252,17 @@ export const usePromptFileHandling = (params?: UsePromptFileHandling) => {
           return true; // Keep this file
         });
       });
+
+      // Call the onFileChange callback to trigger prompt version update with updated files
+      const updatedFiles = files.filter((file) => {
+        if (file.file_id === fileId || file.temp_file_id === fileId) {
+          return false; // Remove this file
+        }
+        return true; // Keep this file
+      });
+      params?.onFileChange?.(updatedFiles);
     },
-    [deleteFileMutation, params?.onFileChange],
+    [params?.onFileChange],
   );
 
   // Sync with external fileSetter when files change