diff --git a/.changeset/fix-active-session-worktree-sweep.md b/.changeset/fix-active-session-worktree-sweep.md
new file mode 100644
index 0000000000..c562e63eb9
--- /dev/null
+++ b/.changeset/fix-active-session-worktree-sweep.md
@@ -0,0 +1,5 @@
+---
+"@runfusion/fusion": patch
+---
+
+Stop self-healing from removing worktrees that are still in use. The idle-worktree and cap-enforcement sweeps now skip any worktree bound to a live executor/merger/step/workflow session, so a checkout is no longer reaped while its task transiently sits in `done` or loses its worktree linkage mid-run.
diff --git a/packages/engine/src/__tests__/self-healing-cli-sessions.test.ts b/packages/engine/src/__tests__/self-healing-cli-sessions.test.ts
index 2dfe8144b3..4e7ae3e79d 100644
--- a/packages/engine/src/__tests__/self-healing-cli-sessions.test.ts
+++ b/packages/engine/src/__tests__/self-healing-cli-sessions.test.ts
@@ -20,6 +20,7 @@ import type { TaskStore } from "@fusion/core";
 import { SelfHealingManager } from "../self-healing.js";
 import * as worktreePool from "../worktree-pool.js";
 import { StuckTaskDetector, type DisposableSession } from "../stuck-task-detector.js";
+import { activeSessionRegistry } from "../active-session-registry.js";
 
 function createStore(settings: Record<string, unknown>): TaskStore & EventEmitter {
   const emitter = new EventEmitter() as TaskStore & EventEmitter;
@@ -46,6 +47,7 @@ describe("self-healing idle-worktree sweeps skip resume-eligible CLI session wor
 
   afterEach(() => {
     rmSync(rootDir, { recursive: true, force: true });
+    activeSessionRegistry.clear();
     vi.restoreAllMocks();
   });
 
@@ -85,6 +87,42 @@ describe("self-healing idle-worktree sweeps skip resume-eligible CLI session wor
     expect(cleaned).toBe(1);
   });
 
+  it("cleanupOrphans skips a worktree backing a live (active-session) executor session", async () => {
+    // FN-4811/FN-5065 regression: a registered idle worktree whose task transiently
+    // sits in "done" (so scanIdleWorktrees lists it) must NOT be reaped while a live
+    // executor/merger/step session is still bound to it — that yanks the checkout out
+    // from under in-flight work ("removed before the work is done").
+    const store = createStore({ recycleWorktrees: false });
+    vi.spyOn(worktreePool, "scanIdleWorktrees").mockResolvedValue([reservedPath, freePath]);
+    const removeSpy = vi.spyOn(worktreePool, "removeWorktree").mockResolvedValue(undefined as never);
+
+    activeSessionRegistry.registerPath(reservedPath, { taskId: "FN-1", kind: "executor", ownerKey: "owner-1" });
+
+    // No isWorktreeResumeReserved seam — protection comes solely from the active session.
+    const manager = new SelfHealingManager(store, { rootDir });
+    const cleaned = await (manager as any).cleanupOrphans();
+
+    const removed = removeSpy.mock.calls.map((c) => (c[0] as { worktreePath: string }).worktreePath);
+    expect(removed).toEqual([freePath]);
+    expect(cleaned).toBe(1);
+  });
+
+  it("enforceWorktreeCap skips a worktree backing a live (active-session) executor session", async () => {
+    mkdirSync(join(worktreesDir, "wt-extra"));
+    const store = createStore({ maxWorktrees: 1, recycleWorktrees: false });
+    vi.spyOn(worktreePool, "scanIdleWorktrees").mockResolvedValue([reservedPath, freePath, join(worktreesDir, "wt-extra")]);
+    const removeSpy = vi.spyOn(worktreePool, "removeWorktree").mockResolvedValue(undefined as never);
+
+    activeSessionRegistry.registerPath(reservedPath, { taskId: "FN-1", kind: "executor", ownerKey: "owner-1" });
+
+    const manager = new SelfHealingManager(store, { rootDir });
+    await (manager as any).enforceWorktreeCap();
+
+    const removed = removeSpy.mock.calls.map((c) => (c[0] as { worktreePath: string }).worktreePath);
+    expect(removed).not.toContain(reservedPath);
+    expect(removed).toContain(freePath);
+  });
+
   it("without the seam predicate, both worktrees are reaped (no behavior change)", async () => {
     const store = createStore({ recycleWorktrees: false });
     vi.spyOn(worktreePool, "scanIdleWorktrees").mockResolvedValue([reservedPath, freePath]);
diff --git a/packages/engine/src/self-healing.ts b/packages/engine/src/self-healing.ts
index ec64edb904..dcbd736c99 100644
--- a/packages/engine/src/self-healing.ts
+++ b/packages/engine/src/self-healing.ts
@@ -8760,6 +8760,14 @@ export class SelfHealingManager {
 
       let cleaned = 0;
       for (const worktreePath of orphaned) {
+        // FN-4811/FN-5065: never reap a worktree bound to a live executor/merger/
+        // step/workflow session. Such a task can sit transiently in "done" (or have
+        // null worktree metadata mid-transition) while the owning process is still
+        // working in the checkout — scanIdleWorktrees would otherwise flag it idle.
+        if (activeSessionRegistry.isPathActive(worktreePath) || activeSessionRegistry.isPathActive(resolve(worktreePath))) {
+          log.log(`[self-healing] deferring idle-sweep for ${worktreePath}: active session present`);
+          continue;
+        }
         // U8: never reclaim a worktree backing a resume-eligible CLI session.
         if (this.isWorktreeResumeReserved(worktreePath)) {
           log.log(`[self-healing] deferring idle-sweep for ${worktreePath}: resume-eligible CLI session present`);
@@ -9218,6 +9226,13 @@ export class SelfHealingManager {
 
       for (const { path: worktreePath } of withMtime) {
         if (removed >= excess) break;
+        // FN-4811/FN-5065: never reap a worktree bound to a live executor/merger/
+        // step/workflow session — cap pressure must not yank a checkout out from
+        // under a process that is still working in it.
+        if (activeSessionRegistry.isPathActive(worktreePath) || activeSessionRegistry.isPathActive(resolve(worktreePath))) {
+          log.log(`[self-healing] cap-enforcement skipping ${worktreePath}: active session present`);
+          continue;
+        }
         // U8: never reclaim a worktree backing a resume-eligible CLI session.
         if (this.isWorktreeResumeReserved(worktreePath)) {
           log.log(`[self-healing] cap-enforcement skipping ${worktreePath}: resume-eligible CLI session present`);