diff --git a/kernel/model/box.go b/kernel/model/box.go
index cb958c483..fa56aa567 100644
--- a/kernel/model/box.go
+++ b/kernel/model/box.go
@@ -503,6 +503,10 @@ func genTreeID(tree *parse.Tree) {
 func FullReindex() {
 	task.AppendTask(task.DatabaseIndexFull, fullReindex)
 	task.AppendTask(task.DatabaseIndexRef, IndexRefs)
+	go func() {
+		sql.WaitForWritingDatabase()
+		ResetVirtualBlockRefCache()
+	}()
 	task.AppendTaskWithTimeout(task.DatabaseIndexEmbedBlock, 30*time.Second, autoIndexEmbedBlock)
 	cache.ClearDocsIAL()
 	cache.ClearBlocksIAL()
diff --git a/kernel/model/index.go b/kernel/model/index.go
index 9a65a2b95..600554c3b 100644
--- a/kernel/model/index.go
+++ b/kernel/model/index.go
@@ -106,23 +106,26 @@ func listSyFiles(dir string) (ret []string) {
 
 func (box *Box) Unindex() {
 	task.AppendTask(task.DatabaseIndex, unindex, box.ID)
-}
-
-func unindex(boxID string) {
-	ids := treenode.RemoveBlockTreesByBoxID(boxID)
-	RemoveRecentDoc(ids)
-	sql.DeleteBoxQueue(boxID)
-
 	go func() {
 		sql.WaitForWritingDatabase()
 		ResetVirtualBlockRefCache()
 	}()
 }
 
+func unindex(boxID string) {
+	ids := treenode.RemoveBlockTreesByBoxID(boxID)
+	RemoveRecentDoc(ids)
+	sql.DeleteBoxQueue(boxID)
+}
+
 func (box *Box) Index() {
 	task.AppendTask(task.DatabaseIndexRef, removeBoxRefs, box.ID)
 	task.AppendTask(task.DatabaseIndex, index, box.ID)
 	task.AppendTask(task.DatabaseIndexRef, IndexRefs)
+	go func() {
+		sql.WaitForWritingDatabase()
+		ResetVirtualBlockRefCache()
+	}()
 }
 
 func removeBoxRefs(boxID string) {
@@ -286,8 +289,6 @@ func IndexRefs() {
 	}
 	logging.LogInfof("resolved refs [%d] in [%dms]", size, time.Now().Sub(start).Milliseconds())
 	util.PushStatusBar(fmt.Sprintf(Conf.Language(55), i))
-
-	ResetVirtualBlockRefCache()
 }
 
 var indexEmbedBlockLock = sync.Mutex{}
diff --git a/kernel/model/repository.go b/kernel/model/repository.go
index 17c90399d..d88991db3 100644
--- a/kernel/model/repository.go
+++ b/kernel/model/repository.go
@@ -51,6 +51,7 @@ import (
 	"github.com/siyuan-note/logging"
 	"github.com/siyuan-note/siyuan/kernel/conf"
 	"github.com/siyuan-note/siyuan/kernel/filesys"
+	"github.com/siyuan-note/siyuan/kernel/sql"
 	"github.com/siyuan-note/siyuan/kernel/task"
 	"github.com/siyuan-note/siyuan/kernel/treenode"
 	"github.com/siyuan-note/siyuan/kernel/util"
@@ -649,6 +650,10 @@ func checkoutRepo(id string) {
 
 	task.AppendTask(task.DatabaseIndexFull, fullReindex)
 	task.AppendTask(task.DatabaseIndexRef, IndexRefs)
+	go func() {
+		sql.WaitForWritingDatabase()
+		ResetVirtualBlockRefCache()
+	}()
 	task.AppendTask(task.ReloadUI, util.ReloadUIResetScroll)
 
 	if syncEnabled {
diff --git a/kernel/model/virutalref.go b/kernel/model/virutalref.go
index f68b3c7bb..e1ba2f4fe 100644
--- a/kernel/model/virutalref.go
+++ b/kernel/model/virutalref.go
@@ -106,8 +106,8 @@ func CacheVirtualBlockRefJob() {
 	task.AppendTask(task.CacheVirtualBlockRef, ResetVirtualBlockRefCache)
 }
 
-func cacheVirtualBlockRef() {
-	virtualBlockRefCache.Del("virtual_ref")
+func ResetVirtualBlockRefCache() {
+	virtualBlockRefCache.Clear()
 	if !Conf.Editor.VirtualBlockRef {
 		return
 	}
@@ -116,11 +116,6 @@ func cacheVirtualBlockRef() {
 	virtualBlockRefCache.Set("virtual_ref", keywords, 1)
 }
 
-func ResetVirtualBlockRefCache() {
-	virtualBlockRefCache.Clear()
-	cacheVirtualBlockRef()
-}
-
 func AddVirtualBlockRefInclude(keyword []string) {
 	if 1 > len(keyword) {
 		return