diff --git a/src/graph.test.ts b/src/graph.test.ts
index ff7037ca..80c8c3f5 100644
--- a/src/graph.test.ts
+++ b/src/graph.test.ts
@@ -58,3 +58,43 @@ describe("Graph colors runtime merge behavior", () => {
     expect(graph.graphColors.anchor?.background).toBe("#222222");
   });
 });
+
+describe("setEntities + waitUsableRectUpdate (pendingEntitiesUpdate fix)", () => {
+  function makeBlock(id: string, x = 0, y = 0): TBlock {
+    return { id, is: "Block", x, y, width: 100, height: 50, selected: false, name: id, anchors: [] };
+  }
+
+  it("resolves waitUsableRectUpdate after setEntities with same block positions", (done) => {
+    const node = document.createElement("div");
+    const block = makeBlock("b1", 10, 20);
+    const graph = new Graph({ blocks: [block], connections: [] }, node);
+    graph.start();
+
+    // Wait for initial hitboxes to settle
+    graph.hitTest.waitUsableRectUpdate(() => {
+      // Call setEntities with the exact same block (same position)
+      graph.setEntities({ blocks: [block], connections: [] });
+
+      // Must resolve after setEntities even though usableRect doesn't change
+      graph.hitTest.waitUsableRectUpdate((rect) => {
+        expect(rect.width).toBeGreaterThan(0);
+        done();
+      });
+    });
+  }, 5000);
+
+  it("resolves waitUsableRectUpdate after setEntities with new blocks", (done) => {
+    const node = document.createElement("div");
+    const graph = new Graph({ blocks: [makeBlock("b1")], connections: [] }, node);
+    graph.start();
+
+    graph.hitTest.waitUsableRectUpdate(() => {
+      graph.setEntities({ blocks: [makeBlock("b2", 200, 200)], connections: [] });
+
+      graph.hitTest.waitUsableRectUpdate((rect) => {
+        expect(rect.x).toBeGreaterThanOrEqual(200);
+        done();
+      });
+    });
+  }, 5000);
+});
diff --git a/src/graph.ts b/src/graph.ts
index 1fb92510..723ec362 100644
--- a/src/graph.ts
+++ b/src/graph.ts
@@ -304,11 +304,10 @@ export class Graph {
     blocks?: TBlock[];
     connections?: TConnection[];
   }>) {
-    // Reset usableRect so that waitUsableRectUpdate (used by zoomToViewPort)
-    // treats hitTest as unstable and waits for new block components to register
-    // their hitboxes. Without this, a stale usableRect can make hitTest appear
-    // stable, causing the zoom callback to fire immediately with wrong data.
-    this.hitTest.resetUsableRect();
+    // Mark hitTest as pending so waitUsableRectUpdate (used by zoomToViewPort)
+    // waits for block components to settle. Unlike resetUsableRect, this does not
+    // clear usableRectTracker, so blocks that haven't moved don't need to re-register.
+    this.hitTest.markPendingUpdate();
     batch(() => {
       this.rootStore.blocksList.setBlocks(blocks || []);
       this.rootStore.connectionsList.setConnections(connections || []);
diff --git a/src/services/HitTest.test.ts b/src/services/HitTest.test.ts
new file mode 100644
index 00000000..63f83682
--- /dev/null
+++ b/src/services/HitTest.test.ts
@@ -0,0 +1,89 @@
+import { Graph } from "../graph";
+
+import { HitBox, HitTest } from "./HitTest";
+
+function makeHitTest(hasBlocks = false): HitTest {
+  const mockGraph = {
+    rootStore: {
+      blocksList: { $blocks: { value: hasBlocks ? [{}] : [] } },
+      connectionsList: { $connections: { value: [] } },
+    },
+  } as unknown as Graph;
+  return new HitTest(mockGraph);
+}
+
+function seedUsableRect(ht: HitTest): void {
+  const fakeHitBox = {
+    affectsUsableRect: true,
+    destroyed: false,
+    minX: 0,
+    minY: 0,
+    maxX: 100,
+    maxY: 100,
+    x: 0,
+    y: 0,
+  } as unknown as HitBox;
+  (ht as unknown as { usableRectTracker: { add(h: HitBox): void } }).usableRectTracker.add(fakeHitBox);
+  (ht as unknown as { updateUsableRect(): void }).updateUsableRect();
+}
+
+/**
+ * Trigger processQueue by queueing a fake hitbox update and flushing.
+ * This mirrors real production code: hitbox updates always precede processQueue.
+ */
+function triggerProcessQueue(ht: HitTest): void {
+  const fakeHitBox = {
+    affectsUsableRect: true,
+    destroyed: false,
+    minX: 0,
+    minY: 0,
+    maxX: 100,
+    maxY: 100,
+    x: 0,
+    y: 0,
+    updateRect(_bbox: unknown): void {
+      // no-op for test fake
+    },
+  } as unknown as HitBox;
+  ht.update(fakeHitBox, { minX: 0, minY: 0, maxX: 100, maxY: 100, x: 0, y: 0 });
+  (ht as unknown as { processQueue: { flush(): void } }).processQueue.flush();
+}
+
+describe("HitTest.markPendingUpdate", () => {
+  it("makes isUnstable true immediately after call", () => {
+    const ht = makeHitTest(true);
+    // Seed non-zero usableRect so zero-rect heuristic doesn't interfere
+    seedUsableRect(ht);
+    expect(ht.isUnstable).toBe(false);
+    ht.markPendingUpdate();
+    expect(ht.isUnstable).toBe(true);
+  });
+
+  it("isUnstable becomes false after processQueue flushes with a hitbox update", () => {
+    const ht = makeHitTest(true);
+    seedUsableRect(ht);
+    ht.markPendingUpdate();
+    expect(ht.isUnstable).toBe(true);
+    // processQueue fires naturally when hitbox updates arrive; simulate that here
+    triggerProcessQueue(ht);
+    expect(ht.isUnstable).toBe(false);
+  });
+
+  it("waitUsableRectUpdate resolves when flag clears, even if usableRect did not change", () => {
+    const ht = makeHitTest(true);
+    seedUsableRect(ht);
+
+    ht.markPendingUpdate();
+    expect(ht.isUnstable).toBe(true);
+
+    let called = false;
+    ht.waitUsableRectUpdate(() => {
+      called = true;
+    });
+    expect(called).toBe(false); // still waiting
+
+    // processQueue fires when hitbox updates arrive (simulated here)
+    triggerProcessQueue(ht);
+    expect(called).toBe(true); // resolved after flag cleared
+  });
+});
diff --git a/src/services/HitTest.ts b/src/services/HitTest.ts
index c6acd30e..4dd53cb0 100644
--- a/src/services/HitTest.ts
+++ b/src/services/HitTest.ts
@@ -59,6 +59,10 @@ export class HitTest extends Emitter {
 
   public readonly $usableRect = signal<TRect>({ x: 0, y: 0, width: 0, height: 0 });
 
+  // Explicit pending flag set by setEntities; cleared when processQueue completes.
+  // Avoids the "zero usableRect = unstable" heuristic for entity replacement.
+  private readonly $pendingEntitiesUpdate = signal(false);
+
   // Single queue replaces all complex state tracking
   protected queue = new Map<HitBox, HitBoxData | null>();
 
@@ -90,10 +94,10 @@ export class HitTest extends Emitter {
 
     // If graph has no elements, it's stable even with zero usableRect
     if (hasZeroUsableRect && !this.hasGraphElements()) {
-      return hasProcessingQueue;
+      return hasProcessingQueue || this.$pendingEntitiesUpdate.value;
     }
 
-    return hasProcessingQueue || hasZeroUsableRect;
+    return hasProcessingQueue || hasZeroUsableRect || this.$pendingEntitiesUpdate.value;
   }
 
   /**
@@ -148,6 +152,7 @@ export class HitTest extends Emitter {
       this.queue.clear();
       this.updateUsableRect();
       this.emit("update", this);
+      this.$pendingEntitiesUpdate.value = false;
     },
     {
       priority: ESchedulerPriority.LOWEST,
@@ -176,6 +181,7 @@ export class HitTest extends Emitter {
     this.interactiveTree.clear();
     this.usableRectTracker.clear();
     this.updateUsableRect();
+    this.$pendingEntitiesUpdate.value = false;
   }
 
   /**
@@ -188,6 +194,20 @@ export class HitTest extends Emitter {
     this.updateUsableRect();
   }
 
+  /**
+   * Mark hitTest as pending an entity update (called by setEntities).
+   * Makes isUnstable = true until processQueue completes.
+   * Does NOT clear usableRectTracker — existing data stays valid.
+   * Does NOT eagerly schedule processQueue — it fires naturally when hitbox
+   * updates arrive (new components register) or when updateBlock forces a hitbox
+   * refresh on existing components. Eager scheduling caused processQueue to run
+   * in the same rAF frame as markPendingUpdate (before MEDIUM/component renders),
+   * clearing $pendingEntitiesUpdate before new block hitboxes were queued.
+   */
+  public markPendingUpdate(): void {
+    this.$pendingEntitiesUpdate.value = true;
+  }
+
   /**
    * Add new HitBox item
    * @param item HitBox item to add
@@ -213,15 +233,25 @@ export class HitTest extends Emitter {
     }
 
     if (this.isUnstable) {
-      const removeListener = this.$usableRect.subscribe(() => {
+      let cleaned = false;
+      let unsubRect: () => void = noop;
+      let unsubPending: () => void = noop;
+      const cleanup = () => {
+        if (cleaned) return;
+        cleaned = true;
+        unsubRect();
+        unsubPending();
+      };
+      const check = () => {
         if (!this.isUnstable) {
-          removeListener();
+          cleanup();
+          // eslint-disable-next-line callback-return
           callback(this.$usableRect.value);
-          return;
         }
-        return;
-      });
-      return removeListener;
+      };
+      unsubRect = this.$usableRect.subscribe(check);
+      unsubPending = this.$pendingEntitiesUpdate.subscribe(check);
+      return cleanup;
     }
     callback(this.$usableRect.value);
     return noop;
diff --git a/src/utils/utils/schedule.ts b/src/utils/utils/schedule.ts
index 70974b1e..6851d64a 100644
--- a/src/utils/utils/schedule.ts
+++ b/src/utils/utils/schedule.ts
@@ -108,9 +108,20 @@ export const debounce = <T extends (...args: Parameters<T>) => void>(
   };
 
   const flush = () => {
-    if (isScheduled && latestArgs) {
-      fn(...latestArgs);
-      cancel();
+    if (isScheduled) {
+      const currentRemoveScheduler = removeScheduler;
+      isScheduled = false;
+      frameCounter = 0;
+      startTime = 0;
+      removeScheduler = null;
+      const args = latestArgs;
+      latestArgs = undefined;
+      // Remove the old scheduler handle BEFORE calling fn() so that any
+      // re-scheduling triggered inside fn() is not accidentally canceled.
+      if (currentRemoveScheduler) {
+        currentRemoveScheduler();
+      }
+      fn(...((args ?? []) as Parameters<T>));
     }
   };