diff --git a/main.js b/main.js
index 2c587b7..71b511d 100644
--- a/main.js
+++ b/main.js
@@ -265,7 +265,7 @@ sessionCache.init({
     setFolderMeta, getAllFolderMeta, getAllMeta, getAllCached, getSetting, getMeta, setName,
   },
 });
-const { readSessionFile, readFolderFromFilesystem, refreshFolder, populateCacheFromFilesystem,
+const { readSessionFile, readFolderFromFilesystem, refreshFolder, reconcileCacheFromFilesystem,
         buildProjectsFromCache, notifyRendererProjectsChanged, sendStatus, populateCacheViaWorker } = sessionCache;
 
 
@@ -416,6 +416,10 @@ ipcMain.handle('get-projects', (_event, showArchived) => {
       return [];
     }
 
+    // Pick up folders changed while the app was closed, or never indexed by an
+    // older build, so sessions/worktrees don't silently go missing. Stat-gated,
+    // so it's cheap when nothing has changed.
+    reconcileCacheFromFilesystem();
     return buildProjectsFromCache(showArchived);
   } catch (err) {
     console.error('Error listing projects:', err);
diff --git a/session-cache.js b/session-cache.js
index f066004..139cf85 100644
--- a/session-cache.js
+++ b/session-cache.js
@@ -153,18 +153,32 @@ function refreshFolder(folder) {
   setFolderMeta(folder, projectPath, getFolderIndexMtimeMs(folderPath));
 }
 
-/** Populate entire cache from filesystem (cold start) */
-function populateCacheFromFilesystem() {
+/**
+ * Reconcile the cache with the filesystem.
+ *
+ * Re-indexes only folders that are new or whose newest .jsonl is newer than what
+ * we last indexed — a cheap, stat-only gate when nothing changed. This is what
+ * keeps sessions from silently going missing: a project folder that changed while
+ * the app was closed, or that predates the build which first indexed it, is
+ * otherwise never picked up, because the cold-start full scan
+ * (populateCacheViaWorker) only runs when the cache is completely empty.
+ */
+function reconcileCacheFromFilesystem() {
   try {
+    const metaMap = getAllFolderMeta();
     const folders = fs.readdirSync(PROJECTS_DIR, { withFileTypes: true })
       .filter(d => d.isDirectory() && d.name !== '.git')
       .map(d => d.name);
 
     for (const folder of folders) {
-      refreshFolder(folder);
+      const meta = metaMap.get(folder);
+      const folderPath = path.join(PROJECTS_DIR, folder);
+      if (!meta || getFolderIndexMtimeMs(folderPath) > (meta.indexMtimeMs || 0)) {
+        refreshFolder(folder);
+      }
     }
   } catch (err) {
-    console.error('Error populating cache:', err);
+    console.error('Error reconciling cache:', err);
   }
 }
 
@@ -383,7 +397,7 @@ module.exports = {
   readSessionFile,
   readFolderFromFilesystem,
   refreshFolder,
-  populateCacheFromFilesystem,
+  reconcileCacheFromFilesystem,
   buildProjectsFromCache,
   notifyRendererProjectsChanged,
   sendStatus,
diff --git a/test/reconcile-cache.test.js b/test/reconcile-cache.test.js
new file mode 100644
index 0000000..8e33f19
--- /dev/null
+++ b/test/reconcile-cache.test.js
@@ -0,0 +1,75 @@
+const test = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('fs');
+const os = require('os');
+const path = require('path');
+
+const sessionCache = require('../session-cache');
+const { getFolderIndexMtimeMs } = require('../folder-index-state');
+
+// Minimal valid session transcript: one line carries `cwd` (for deriveProjectPath)
+// and a user message (so readSessionFile yields a non-null session).
+function writeSession(folderPath, cwd) {
+  fs.mkdirSync(folderPath, { recursive: true });
+  const line = JSON.stringify({ type: 'user', cwd, message: { role: 'user', content: 'hello' } });
+  fs.writeFileSync(path.join(folderPath, 'session.jsonl'), line + '\n', 'utf8');
+}
+
+// In-memory fake of the db layer that init() expects, recording which folders
+// actually got (re)indexed (i.e. had refreshFolder do work and upsert sessions).
+function makeFakeDb(metaMap) {
+  const indexedFolders = new Set();
+  return {
+    indexedFolders,
+    db: {
+      deleteCachedFolder() {},
+      getCachedByFolder() { return []; },
+      upsertCachedSessions(sessions) { for (const s of sessions) indexedFolders.add(s.folder); },
+      deleteCachedSession() {},
+      deleteSearchFolder() {},
+      deleteSearchSession() {},
+      upsertSearchEntries() {},
+      setFolderMeta(folder, projectPath, indexMtimeMs) { metaMap.set(folder, { folder, projectPath, indexMtimeMs }); },
+      getAllFolderMeta() { return metaMap; },
+      getAllMeta() { return new Map(); },
+      getAllCached() { return []; },
+      getSetting() { return {}; },
+      getMeta() { return null; },
+      setName() {},
+    },
+  };
+}
+
+test('reconcileCacheFromFilesystem indexes new and stale folders but skips up-to-date ones', () => {
+  const projectsDir = fs.mkdtempSync(path.join(os.tmpdir(), 'switchboard-reconcile-'));
+  try {
+    // never-indexed (no meta), stale (meta older than disk), and up-to-date folders
+    writeSession(path.join(projectsDir, 'proj-new'), '/tmp/proj-new');
+    writeSession(path.join(projectsDir, 'proj-stale'), '/tmp/proj-stale');
+    writeSession(path.join(projectsDir, 'proj-current'), '/tmp/proj-current');
+
+    const metaMap = new Map();
+    metaMap.set('proj-stale', { folder: 'proj-stale', projectPath: '/tmp/proj-stale', indexMtimeMs: 0 });
+    metaMap.set('proj-current', {
+      folder: 'proj-current', projectPath: '/tmp/proj-current',
+      indexMtimeMs: getFolderIndexMtimeMs(path.join(projectsDir, 'proj-current')),
+    });
+
+    const fake = makeFakeDb(metaMap);
+    sessionCache.init({
+      PROJECTS_DIR: projectsDir,
+      activeSessions: new Map(),
+      getMainWindow: () => null,
+      log: console,
+      db: fake.db,
+    });
+
+    sessionCache.reconcileCacheFromFilesystem();
+
+    assert.ok(fake.indexedFolders.has('proj-new'), 'new folder should be indexed');
+    assert.ok(fake.indexedFolders.has('proj-stale'), 'stale folder (older indexMtimeMs) should be re-indexed');
+    assert.ok(!fake.indexedFolders.has('proj-current'), 'up-to-date folder should be skipped');
+  } finally {
+    fs.rmSync(projectsDir, { recursive: true, force: true });
+  }
+});