diff --git a/packages/coding-agent/src/memories/index.ts b/packages/coding-agent/src/memories/index.ts
index 81b5777b0cc..730f58eacfc 100644
--- a/packages/coding-agent/src/memories/index.ts
+++ b/packages/coding-agent/src/memories/index.ts
@@ -508,7 +508,13 @@ async function runPhase2(options: MemoryStartupOptions): Promise<void> {
 		await syncPhase2Artifacts(memoryRoot, outputs);
 		if (!isMemoryStartupActive(options)) return;
 		if (outputs.length === 0) {
-			await cleanupConsolidatedArtifacts(memoryRoot);
+			// Never wipe consolidated artifacts for an empty input: the scope
+			// may simply have no outputs yet (or its outputs landed under a
+			// sibling scope key, e.g. a case-variant cwd on Windows), while a
+			// live MEMORY.md / memory_summary.md / skills/ from a prior run —
+			// or a racing scope sharing this directory — is still valid. The
+			// destructive cleanup previously deleted those on every empty
+			// Phase 2, stranding and erasing real consolidations (#12596).
 			if (!isMemoryStartupActive(options)) return;
 			const marked = markGlobalPhase2Succeeded(db, {
 				ownershipToken: claim.ownershipToken,
@@ -861,12 +867,6 @@ async function syncPhase2Artifacts(memoryRoot: string, outputs: Stage1OutputRow[
 	await Bun.write(path.join(memoryRoot, "raw_memories.md"), rawBody);
 }
 
-async function cleanupConsolidatedArtifacts(memoryRoot: string): Promise<void> {
-	await fs.rm(path.join(memoryRoot, "MEMORY.md"), { force: true });
-	await fs.rm(path.join(memoryRoot, "memory_summary.md"), { force: true });
-	await fs.rm(path.join(memoryRoot, "skills"), { recursive: true, force: true });
-}
-
 function buildRawMemoriesMarkdown(outputs: Stage1OutputRow[]): string {
 	if (outputs.length === 0) {
 		return "# Raw Memories\n\nNo raw memories yet.\n";
diff --git a/packages/coding-agent/test/memories-runtime.test.ts b/packages/coding-agent/test/memories-runtime.test.ts
index 8ef810e02ee..7aa8e050051 100644
--- a/packages/coding-agent/test/memories-runtime.test.ts
+++ b/packages/coding-agent/test/memories-runtime.test.ts
@@ -398,7 +398,7 @@ describe("memories runtime", () => {
 		expect(raw.indexOf("## thread-b")).toBeLessThan(raw.indexOf("## thread-a"));
 	});
 
-	test("phase2 empty-input cleanup removes consolidated files and skills dir", async () => {
+	test("phase2 empty-input preserves consolidated files and skills dir (issue #12596)", async () => {
 		const fx = await createFixture();
 		const memoryRoot = getMemoryRoot(fx.agentDir, fx.session.sessionManager.getCwd());
 		await fs.mkdir(path.join(memoryRoot, "skills", "legacy"), { recursive: true });
@@ -420,10 +420,13 @@ describe("memories runtime", () => {
 			taskDepth: 0,
 		});
 
-		await settle(fx.whenSettled, "phase2 empty-input cleanup");
-		expect(await Bun.file(path.join(memoryRoot, "MEMORY.md")).exists()).toBe(false);
-		expect(await Bun.file(path.join(memoryRoot, "memory_summary.md")).exists()).toBe(false);
-		expect(await Bun.file(path.join(memoryRoot, "skills")).exists()).toBe(false);
+		await settle(fx.whenSettled, "phase2 empty-input preservation");
+		// An empty Phase 2 must not wipe live consolidations: outputs may land
+		// later (or under a sibling scope key), and the artifacts on disk are
+		// still valid. Previously this path deleted them.
+		expect(await Bun.file(path.join(memoryRoot, "MEMORY.md")).exists()).toBe(true);
+		expect(await Bun.file(path.join(memoryRoot, "memory_summary.md")).exists()).toBe(true);
+		expect(await Bun.file(path.join(memoryRoot, "skills", "legacy", "SKILL.md")).exists()).toBe(true);
 		expect((await fs.readFile(path.join(memoryRoot, "raw_memories.md"), "utf8")).trim()).toBe(
 			"# Raw Memories\n\nNo raw memories yet.",
 		);