diff --git a/scripts/lib/codex-legacy-sync.js b/scripts/lib/codex-legacy-sync.js
index f228afb20..e12a69aec 100644
--- a/scripts/lib/codex-legacy-sync.js
+++ b/scripts/lib/codex-legacy-sync.js
@@ -475,6 +475,26 @@ function listLegacyCandidates(codexHome) {
   return candidates;
 }
 
+function hasMarkerBlock(codexHome) {
+  const agentsPath = path.join(codexHome, 'AGENTS.md');
+  try {
+    const snapshot = readRegularFileNoFollow(agentsPath, 'utf8');
+    if (snapshot) {
+      const stripped = stripMarkerBlock(snapshot.content);
+      return stripped !== snapshot.content;
+    }
+  } catch (_error) {
+    // Non-regular or unreadable AGENTS.md is not a clean marker signal.
+  }
+  return false;
+}
+
+function detectLegacyCodexSync(codexHome) {
+  const resolvedCodexHome = path.resolve(codexHome || process.env.CODEX_HOME || path.join(process.env.HOME || os.homedir(), '.codex'));
+  if (readStateIfPresent(getStatePath(resolvedCodexHome))) return true;
+  return hasMarkerBlock(resolvedCodexHome);
+}
+
 function uninstallLegacyCodexSync(options = {}) {
   const codexHome = path.resolve(options.codexHome || process.env.CODEX_HOME || path.join(process.env.HOME || os.homedir(), '.codex'));
   const statePath = getStatePath(codexHome);
@@ -498,13 +518,17 @@ function uninstallLegacyCodexSync(options = {}) {
         }
       }
     } catch (_error) {
-      retainedPaths.push(agentsPath);
+      if (_error.code !== 'ENOENT') retainedPaths.push(agentsPath);
     } finally {
       if (openedAgents) fs.closeSync(openedAgents.descriptor);
     }
     retainedPaths.push(...listLegacyCandidates(codexHome));
+    const hasWork = plannedRemovals.length > 0 || removedPaths.length > 0;
+    const status = dryRun
+      ? (hasWork || retainedPaths.length > 0 ? 'planned' : 'not-found')
+      : (retainedPaths.length > 0 ? 'partial' : (hasWork ? 'uninstalled' : 'not-found'));
     return {
-      status: dryRun ? 'planned' : retainedPaths.length > 0 ? 'partial' : plannedRemovals.length > 0 ? 'uninstalled' : 'not-found',
+      status,
       statePath: null,
       plannedRemovals,
       removedPaths,
@@ -594,6 +618,7 @@ module.exports = {
   END_MARKER,
   SCHEMA,
   beginLegacySyncState,
+  detectLegacyCodexSync,
   finalizeLegacySyncState,
   getStatePath,
   recordLegacySyncPath,
diff --git a/scripts/uninstall.js b/scripts/uninstall.js
index ff515aacc..eaba93c68 100644
--- a/scripts/uninstall.js
+++ b/scripts/uninstall.js
@@ -5,7 +5,10 @@ const path = require('path');
 const { uninstallInstalledStates } = require('./lib/install-lifecycle');
 const { SUPPORTED_INSTALL_TARGETS } = require('./lib/install-manifests');
 const { exitFeedbackLines } = require('./lib/feedback-links');
-const { uninstallLegacyCodexSync } = require('./lib/codex-legacy-sync');
+const {
+  detectLegacyCodexSync,
+  uninstallLegacyCodexSync,
+} = require('./lib/codex-legacy-sync');
 
 function showHelp(exitCode = 0) {
   console.log(`
@@ -90,12 +93,8 @@ function printHuman(result) {
   }
 }
 
-function detectLegacyCodexSync(codexHome) {
-  const probe = uninstallLegacyCodexSync({
-    codexHome,
-    dryRun: true,
-  });
-  return probe.status !== 'not-found';
+function legacyCodexSyncDetected(codexHome) {
+  return detectLegacyCodexSync(codexHome);
 }
 
 function printLegacy(result, dryRun) {
@@ -149,7 +148,7 @@ async function main() {
       if (
         result.results.length === 0
         && includesCodexTarget(options.targets)
-        && detectLegacyCodexSync(codexHomePath())
+        && legacyCodexSyncDetected(codexHomePath())
       ) {
         result = uninstallLegacyCodexSync({
           codexHome: codexHomePath(),
diff --git a/tests/scripts/uninstall.test.js b/tests/scripts/uninstall.test.js
index aeae14ed2..b42c6c2f2 100644
--- a/tests/scripts/uninstall.test.js
+++ b/tests/scripts/uninstall.test.js
@@ -418,6 +418,56 @@ function runTests() {
     }
   })) passed++; else failed++;
 
+  if (test('does not misclassify a clean Codex home as a legacy install', () => {
+    const homeDir = createTempDir('uninstall-clean-codex-home-');
+    const projectRoot = createTempDir('uninstall-clean-codex-project-');
+
+    try {
+      const codexHome = path.join(homeDir, '.codex');
+      const configPath = path.join(codexHome, 'config.toml');
+      const conversationPath = path.join(codexHome, 'conversations', 'keep-me.md');
+
+      fs.mkdirSync(codexHome, { recursive: true });
+      fs.writeFileSync(configPath, 'model = "user"\n');
+      fs.mkdirSync(path.dirname(conversationPath), { recursive: true });
+      fs.writeFileSync(conversationPath, 'conversation history');
+
+      const uninstallResult = run([], { cwd: projectRoot, homeDir });
+      assert.strictEqual(uninstallResult.code, 0, uninstallResult.stderr);
+      assert.ok(uninstallResult.stdout.includes('No ECC install-state files found'), uninstallResult.stdout);
+      assert.ok(!uninstallResult.stdout.includes('Legacy Codex sync cleanup summary'), uninstallResult.stdout);
+      assert.strictEqual(fs.readFileSync(configPath, 'utf8'), 'model = "user"\n');
+      assert.strictEqual(fs.readFileSync(conversationPath, 'utf8'), 'conversation history');
+    } finally {
+      cleanup(homeDir);
+      cleanup(projectRoot);
+    }
+  })) passed++; else failed++;
+
+  if (test('explicit --legacy-codex-sync on a clean home reports not-found without removing files', () => {
+    const homeDir = createTempDir('uninstall-legacy-clean-home-');
+    const projectRoot = createTempDir('uninstall-legacy-clean-project-');
+
+    try {
+      const codexHome = path.join(homeDir, '.codex');
+      const configPath = path.join(codexHome, 'config.toml');
+
+      fs.mkdirSync(codexHome, { recursive: true });
+      fs.writeFileSync(configPath, 'model = "user"\n');
+
+      const uninstallResult = run(['--legacy-codex-sync', '--json'], { cwd: projectRoot, homeDir });
+      assert.strictEqual(uninstallResult.code, 0, uninstallResult.stderr);
+      const parsed = JSON.parse(uninstallResult.stdout);
+      assert.strictEqual(parsed.status, 'not-found');
+      assert.deepStrictEqual(parsed.plannedRemovals, []);
+      assert.deepStrictEqual(parsed.retainedPaths, []);
+      assert.strictEqual(fs.readFileSync(configPath, 'utf8'), 'model = "user"\n');
+    } finally {
+      cleanup(homeDir);
+      cleanup(projectRoot);
+    }
+  })) passed++; else failed++;
+
   console.log(`\nResults: Passed: ${passed}, Failed: ${failed}`);
   process.exit(failed > 0 ? 1 : 0);
 }