diff --git a/frontend/src/lib/components/graph/FlowGraphV2.svelte b/frontend/src/lib/components/graph/FlowGraphV2.svelte
index 74430cffde..184c4e2170 100644
--- a/frontend/src/lib/components/graph/FlowGraphV2.svelte
+++ b/frontend/src/lib/components/graph/FlowGraphV2.svelte
@@ -734,11 +734,9 @@
 		return false
 	}
 
-	// Clear SvelteFlow's internal selection by creating new nodes array
 	function clearFlowSelection() {
-		// xyflow owns `selected` on the objects it was handed, and drops it only when it sees a
-		// node it does not recognise. Serving the cached mapping back would hand it the very
-		// object it marked selected, so the clear has to go through fresh objects.
+		// Resetting the cache and reassigning `nodes` hands xyflow objects it has not seen, the
+		// only lever on its selection available from our own array.
 		offsetNodeCache = new WeakMap<Node, Node>()
 		nodes = nodes.map((node) => {
 			if (node.selected) {
@@ -1411,7 +1409,7 @@
 				/>
 
 				<!-- SelectionTool for handling selection changes and filtering -->
-				<SelectionTool {selectionManager} clearGraphSelection={clearFlowSelection} />
+				<SelectionTool {selectionManager} />
 
 				{#if leftHeader}
 					<div class="absolute top-2 left-2 z-10">
diff --git a/frontend/src/lib/components/graph/SelectionTool.svelte b/frontend/src/lib/components/graph/SelectionTool.svelte
index dd5033bf55..5fd6147c71 100644
--- a/frontend/src/lib/components/graph/SelectionTool.svelte
+++ b/frontend/src/lib/components/graph/SelectionTool.svelte
@@ -4,16 +4,18 @@
 	import type { SelectionManager } from './selectionUtils.svelte'
 	interface Props {
 		selectionManager: SelectionManager
-		clearGraphSelection: () => void
 	}
 
-	let { selectionManager, clearGraphSelection }: Props = $props()
+	let { selectionManager }: Props = $props()
 
-	untrack(() => selectionManager).setClearGraphSelection(untrack(() => clearGraphSelection))
-
-	// Get store to access selectionRect
 	const store = useStore()
 
+	// Clear through xyflow's store, never by handing it fresh node objects: replacing them
+	// re-creates every node's DOM, and a click whose node is rebuilt between pointerdown and
+	// release retargets to the pane, which clears the selection that same gesture just made.
+	// While xyflow holds a selection, useOnSelectionChange below re-broadcasts it over ours.
+	untrack(() => selectionManager).setClearGraphSelection(() => store.unselectNodesAndEdges())
+
 	// Handle selection changes from SvelteFlow
 	useOnSelectionChange(({ nodes: selectedNodes, edges: _selectedEdges }) => {
 		// Notes are already non-selectable, so no filtering needed
diff --git a/frontend/src/lib/components/graph/graphContext.ts b/frontend/src/lib/components/graph/graphContext.ts
index a6245769cf..567bfb6348 100644
--- a/frontend/src/lib/components/graph/graphContext.ts
+++ b/frontend/src/lib/components/graph/graphContext.ts
@@ -12,6 +12,8 @@ export type GraphContext = {
 	showAssets: Writable<boolean | undefined>
 	noteManager?: NoteManager
 	moveManager?: MoveManager
+	/** Clears xyflow's selection by replacing every node object, so only for callers that rebuild
+	 *  the graph anyway. A selection change must use `selectionManager` instead. */
 	clearFlowSelection?: () => void
 	yOffset?: number
 	diffManager: FlowDiffManager