diff --git a/frontend/src/pages/DatabaseSchema.tsx b/frontend/src/pages/DatabaseSchema.tsx
index 024f801..cce08fd 100644
--- a/frontend/src/pages/DatabaseSchema.tsx
+++ b/frontend/src/pages/DatabaseSchema.tsx
@@ -376,9 +376,19 @@ export default function DatabaseSchema() {
   const [nodes, setNodes, onNodesChange] = useNodesState<Node>([]);
   const [edges, setEdges, onEdgesChange] = useEdgesState<Edge>([]);
 
+  // Reset and rebuild when filtered schema changes
   useEffect(() => {
-    setNodes(layoutedNodes);
-    setEdges(layoutedEdges);
+    // Clear first to avoid stale edges
+    setNodes([]);
+    setEdges([]);
+
+    // Then set new layout after a tick
+    if (layoutedNodes.length > 0) {
+      requestAnimationFrame(() => {
+        setNodes(layoutedNodes);
+        setEdges(layoutedEdges);
+      });
+    }
   }, [layoutedNodes, layoutedEdges, setNodes, setEdges]);
 
   const getSearchIcon = (type: SearchResult['type']) => {