diff --git a/web/app/components/workflow/hooks/use-nodes-interactions.ts b/web/app/components/workflow/hooks/use-nodes-interactions.ts
index 6a9b708eca..263f7f8e67 100644
--- a/web/app/components/workflow/hooks/use-nodes-interactions.ts
+++ b/web/app/components/workflow/hooks/use-nodes-interactions.ts
@@ -1471,11 +1471,10 @@ export const useNodesInteractions = () => {
 
     const {
       getNodes,
-      setNodes,
       edges,
-      setEdges,
     } = store.getState()
     const nodes = getNodes()
+    const { setNodes, setEdges } = useCollaborationStore.getState()
     const currentNode = nodes.find(node => node.id === nodeId)!
     const connectedEdges = getConnectedEdges([currentNode], edges)
     const nodesConnectedSourceOrTargetHandleIdsMap = getNodesConnectedSourceOrTargetHandleIdsMap(
@@ -1497,18 +1496,6 @@ export const useNodesInteractions = () => {
       return draft.filter(edge => !connectedEdges.find(connectedEdge => connectedEdge.id === edge.id))
     })
     setEdges(newEdges)
-
-    const { nodesMap, edgesMap, loroDoc } = useCollaborationStore.getState()
-    if (nodesMap && edgesMap && loroDoc) {
-      // newNodes.forEach((node) => {
-      //   nodesMap.set(node.id, node)
-      // })
-      connectedEdges.forEach((edge) => {
-        edgesMap.delete(edge.id)
-      })
-      loroDoc.commit()
-    }
-
     handleSyncWorkflowDraft()
     saveStateToHistory(WorkflowHistoryEvent.EdgeDelete)
   }, [store, getNodesReadOnly, handleSyncWorkflowDraft, saveStateToHistory])
diff --git a/web/app/components/workflow/store/collaboration-store.ts b/web/app/components/workflow/store/collaboration-store.ts
index c9fe1f0e44..649ae6a008 100644
--- a/web/app/components/workflow/store/collaboration-store.ts
+++ b/web/app/components/workflow/store/collaboration-store.ts
@@ -1,6 +1,7 @@
 import { create } from 'zustand'
 
 import { LoroDoc } from 'loro-crdt'
+import { isEqual } from 'lodash-es'
 import type { Edge, Node } from '../types'
 import { useWebSocketStore } from './websocket-store'
 
@@ -48,6 +49,9 @@ type CollaborationStore = {
   edges: Edge[]
   updateNodes?: () => void
   updateEdges?: () => void
+
+  setNodes: (newNodes: Node[]) => void
+  setEdges: (newEdges: Edge[]) => void
   initCollaboration: (appId: string) => void
   destroyCollaboration: () => void
 }
@@ -60,6 +64,78 @@ export const useCollaborationStore = create<CollaborationStore>((set, get) => ({
   nodes: [],
   edges: [],
 
+  setNodes: (newNodes: Node[]) => {
+    const { nodes: oldNodes, nodesMap, loroDoc } = get()
+
+    const oldNodesMap = new Map(oldNodes.map(node => [node.id, node]))
+    const newNodesMap = new Map(newNodes.map(node => [node.id, node]))
+
+    const getPersistentNodeData = (node: Node) => {
+    const { data, ...rest } = node
+    const filteredData = Object.fromEntries(
+      Object.entries(data).filter(([key]) =>
+        !key.startsWith('_') && key !== 'selected',
+      ),
+    )
+
+      return {
+        ...rest,
+        data: filteredData,
+      }
+    }
+
+    // delete
+    oldNodes.forEach((oldNode) => {
+      if (!newNodesMap.has(oldNode.id))
+        nodesMap.delete(oldNode.id)
+    })
+
+    newNodes.forEach((newNode) => {
+      const oldNode = oldNodesMap.get(newNode.id)
+      if (!oldNode) {
+        // add
+        nodesMap.set(newNode.id, getPersistentNodeData(newNode))
+      }
+ else {
+        const oldPersistentData = getPersistentNodeData(oldNode)
+        const newPersistentData = getPersistentNodeData(newNode)
+
+        if (!isEqual(oldPersistentData, newPersistentData)) {
+          // update
+          nodesMap.set(newNode.id, newPersistentData)
+        }
+      }
+    })
+    loroDoc.commit()
+  },
+
+  setEdges: (newEdges: Edge[]) => {
+    const { edges: oldEdges, edgesMap, loroDoc } = get()
+
+    const oldEdgesMap = new Map(oldEdges.map(edge => [edge.id, edge]))
+    const newEdgesMap = new Map(newEdges.map(edge => [edge.id, edge]))
+
+    // delete
+    oldEdges.forEach((oldEdge) => {
+      if (!newEdgesMap.has(oldEdge.id))
+        edgesMap.delete(oldEdge.id)
+    })
+
+    newEdges.forEach((newEdge) => {
+      const oldEdge = oldEdgesMap.get(newEdge.id)
+      if (!oldEdge) {
+        // add
+        edgesMap.set(newEdge.id, newEdge)
+      }
+ else if (!isEqual(oldEdge, newEdge)) {
+        // update
+        edgesMap.set(newEdge.id, newEdge)
+      }
+    })
+
+    loroDoc.commit()
+  },
+
   initCollaboration: (appId: string) => {
     const { getSocket } = useWebSocketStore.getState()
     const socket = getSocket(appId)
diff --git a/web/app/components/workflow/store/workflow/workflow-draft-slice.ts b/web/app/components/workflow/store/workflow/workflow-draft-slice.ts
index ec28debee2..c6d62e4628 100644
--- a/web/app/components/workflow/store/workflow/workflow-draft-slice.ts
+++ b/web/app/components/workflow/store/workflow/workflow-draft-slice.ts
@@ -28,7 +28,7 @@ export const createWorkflowDraftSlice: StateCreator<WorkflowDraftSliceShape> = s
   setBackupDraft: backupDraft => set(() => ({ backupDraft })),
   debouncedSyncWorkflowDraft: debounce((syncWorkflowDraft) => {
     syncWorkflowDraft()
-  }, 5000),
+  }, 500000),
   syncWorkflowDraftHash: '',
   setSyncWorkflowDraftHash: syncWorkflowDraftHash => set(() => ({ syncWorkflowDraftHash })),
   isSyncingWorkflowDraft: false,