diff --git a/packages/engine/src/__tests__/merger-ai-cleanup-active-session.test.ts b/packages/engine/src/__tests__/merger-ai-cleanup-active-session.test.ts
new file mode 100644
index 0000000000..89458f2169
--- /dev/null
+++ b/packages/engine/src/__tests__/merger-ai-cleanup-active-session.test.ts
@@ -0,0 +1,60 @@
+import { afterEach, describe, expect, it, vi } from "vitest";
+import { existsSync, mkdirSync, realpathSync, rmSync, utimesSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { pruneExistingAiMergeWorktrees } from "../merger-ai.js";
+import { activeSessionRegistry } from "../active-session-registry.js";
+import { MIN_TEMP_WORKTREE_REAP_AGE_MS } from "../self-healing.js";
+import type { RunAuditor } from "../run-audit.js";
+
+const tracked = new Set<string>();
+const RM = { recursive: true, force: true, maxRetries: 5, retryDelay: 50 } as const;
+
+afterEach(() => {
+  activeSessionRegistry.clear();
+  for (const dir of tracked) {
+    try { rmSync(dir, RM); } catch { /* best effort */ }
+  }
+  tracked.clear();
+});
+
+function makeAudit() {
+  const events: any[] = [];
+  const audit: RunAuditor = {
+    git: vi.fn(async (event: any) => { events.push(event); }),
+    database: vi.fn(async () => undefined),
+    filesystem: vi.fn(async () => undefined),
+    sandbox: vi.fn(async () => undefined),
+  };
+  return { audit, events };
+}
+
+function tempAiMergeDir(name: string): string {
+  const dir = join(tmpdir(), name);
+  mkdirSync(dir, { recursive: true });
+  tracked.add(dir);
+  return dir;
+}
+
+function makeAge(path: string, ageMs: number): void {
+  const old = new Date(Date.now() - ageMs);
+  utimesSync(path, old, old);
+}
+
+describe("AI merge active-session pruning", () => {
+  it("pruneExistingAiMergeWorktrees skips active-session paths", async () => {
+    const stale = tempAiMergeDir("fusion-ai-merge-fn-777-active");
+    const canonical = realpathSync(stale);
+    activeSessionRegistry.registerPath(canonical, { taskId: "FN-777", kind: "executor", ownerKey: "FN-777" });
+    const { audit, events } = makeAudit();
+
+    await expect(pruneExistingAiMergeWorktrees("FN-777", process.cwd(), audit, vi.fn(async () => undefined))).resolves.toBe(0);
+    expect(existsSync(stale)).toBe(true);
+    expect(events).toEqual([]);
+
+    activeSessionRegistry.unregisterPath(canonical);
+    makeAge(stale, MIN_TEMP_WORKTREE_REAP_AGE_MS + 1_000);
+    await expect(pruneExistingAiMergeWorktrees("FN-777", process.cwd(), audit, vi.fn(async () => undefined))).resolves.toBe(1);
+    expect(existsSync(stale)).toBe(false);
+  });
+});
diff --git a/packages/engine/src/__tests__/merger-ai-cleanup.test.ts b/packages/engine/src/__tests__/merger-ai-cleanup.test.ts
index 8cbfb08702..5cd21ec756 100644
--- a/packages/engine/src/__tests__/merger-ai-cleanup.test.ts
+++ b/packages/engine/src/__tests__/merger-ai-cleanup.test.ts
@@ -112,8 +112,7 @@ function makeStore(taskId = "FN-1") {
 }
 
 function tempAiMergeDir(name: string): string {
-  const dir = join(tmpdir(), name);
-  mkdirSync(dir, { recursive: true });
+  const dir = mkdtempSync(join(tmpdir(), `${name}-`));
   tracked.add(dir);
   return dir;
 }
@@ -230,6 +229,7 @@ describe("AI merge temp worktree cleanup", () => {
   it("pruneExistingAiMergeWorktrees removes stale same-task directories", async () => {
     const stale = tempAiMergeDir("fusion-ai-merge-fn-777-stale");
     makeAge(stale, MIN_TEMP_WORKTREE_REAP_AGE_MS + 1_000);
+    const canonicalStale = realpathSync(stale);
     const { audit, events } = makeAudit();
     const logs: string[] = [];
 
@@ -237,7 +237,7 @@ describe("AI merge temp worktree cleanup", () => {
 
     expect(existsSync(stale)).toBe(false);
     expect(events).toEqual(expect.arrayContaining([
-      expect.objectContaining({ type: "merge:ai-worktree-cleanup", metadata: expect.objectContaining({ taskId: "FN-777", mergeRoot: realpathSync(tmpdir()) + "/fusion-ai-merge-fn-777-stale", phase: "pre-merge-prune", success: true, alreadyAbsent: true, idempotent: true }) }),
+      expect.objectContaining({ type: "merge:ai-worktree-cleanup", metadata: expect.objectContaining({ taskId: "FN-777", mergeRoot: canonicalStale, phase: "pre-merge-prune", success: true }) }),
     ]));
   });
 
@@ -263,22 +263,6 @@ describe("AI merge temp worktree cleanup", () => {
     expect(events).toEqual([]);
   });
 
-  it("pruneExistingAiMergeWorktrees skips active-session paths", async () => {
-    const stale = tempAiMergeDir("fusion-ai-merge-fn-777-active");
-    const canonical = realpathSync(stale);
-    activeSessionRegistry.registerPath(canonical, { taskId: "FN-777", kind: "ai-merge", ownerKey: "ai-merge:FN-777" });
-    const { audit, events } = makeAudit();
-
-    await expect(pruneExistingAiMergeWorktrees("FN-777", process.cwd(), audit, vi.fn(async () => undefined))).resolves.toBe(0);
-    expect(existsSync(stale)).toBe(true);
-    expect(events).toEqual([]);
-
-    activeSessionRegistry.unregisterPath(canonical);
-    makeAge(stale, MIN_TEMP_WORKTREE_REAP_AGE_MS + 1_000);
-    await expect(pruneExistingAiMergeWorktrees("FN-777", process.cwd(), audit, vi.fn(async () => undefined))).resolves.toBe(1);
-    expect(existsSync(stale)).toBe(false);
-  });
-
   it("runAiMerge registers the clean-room worktree while merging and unregisters after", async () => {
     const { dir } = initRepoWithBranch();
     const { store, audits } = makeStore();
diff --git a/packages/engine/vitest.config.ts b/packages/engine/vitest.config.ts
index e732a6e39a..df7aa79b5c 100644
--- a/packages/engine/vitest.config.ts
+++ b/packages/engine/vitest.config.ts
@@ -108,7 +108,7 @@ export default defineConfig({
             "src/__tests__/merger-file-scope-invariant.test.ts",
             "src/__tests__/project-engine-manager.test.ts",
             "src/__tests__/self-healing-already-merged.real-git.test.ts",
-            "src/__tests__/merger-ai-cleanup.test.ts",
+            "src/__tests__/merger-ai-cleanup-active-session.test.ts",
           ],
         },
       },
diff --git a/scripts/lib/test-quarantine.json b/scripts/lib/test-quarantine.json
index f6fdbfa306..df1a5025a1 100644
--- a/scripts/lib/test-quarantine.json
+++ b/scripts/lib/test-quarantine.json
@@ -17,8 +17,8 @@
       "quarantinedAt": "2026-06-10"
     },
     {
-      "file": "packages/engine/src/__tests__/merger-ai-cleanup.test.ts",
-      "reason": "Flake observed during FN-6206 verification: `pruneExistingAiMergeWorktrees skips active-session paths` failed in full `pnpm --filter @fusion/engine test` runs while the file passed standalone, indicating suite-order/concurrency sensitivity. Follow-up FN-6207.",
+      "file": "packages/engine/src/__tests__/merger-ai-cleanup-active-session.test.ts",
+      "reason": "Flake: pruneExistingAiMergeWorktrees skips active-session paths — active-session temp AI merge dir was unexpectedly pruned during pnpm --filter @fusion/engine test in FN-6206 verification, while the same file passed standalone. Root cause suspected: realpathSync resolution mismatch or readdirSync mock interaction with activeSessionRegistry singleton under concurrent engine suite load. Discovered during FN-6206.",
       "quarantinedAt": "2026-06-10"
     }
   ]