diff --git a/Agent.md b/Agent.md
index 82d4e6e..2817b5b 100644
--- a/Agent.md
+++ b/Agent.md
@@ -118,7 +118,7 @@ Community needs voiced in HN agent-UI discussions map directly to EMRG's design:
 pkill -f "emrg.server"; rm -f ~/.emrg/emrgd.port; python -m emrg
 ```
 
-Python: `uv run pytest tests/ -v` (799) — import check: `uv run python -c "from emrg.client.app import run_client"`
+Python: `uv run pytest tests/ -v` (800) — import check: `uv run python -c "from emrg.client.app import run_client"`
 GUI: `cd emrg/gui && npm test` (236: 44 daemon_client + 19 conn-manager + 22 app-commands + 114 renderer smoke + 15 i18n + 7 integration + 3 commands + 5 build-config + 7 gui-state) — syntax: `node --check main.js preload.js daemon_client.js renderer/js/*.js`
 CI: `uv run pytest` (ubuntu + **windows-2025 matrix** — Windows pytest 回归在 PR CI 即失败，v0.2.29 教训 #725) + GUI tests + **actionlint workflow lint** (`rhysd/actionlint@v1.7.12` gate, #444 — workflow 解析错误在 PR CI 即失败，如 `if:` secrets 上下文)
 Re-trigger: `scripts/re-trigger-ci.sh [branch]` (workflow_dispatch, #527 — 替代空 commit 重触发：Actions outage 会整段丢弃 push 事件，dispatch 走 API 路径不受影响)
diff --git a/emrg/sessions_index.py b/emrg/sessions_index.py
index 0ff5b36..549b241 100644
--- a/emrg/sessions_index.py
+++ b/emrg/sessions_index.py
@@ -158,6 +158,9 @@ def rebuild_sessions_index(
     Scans ``config_root`` recursively (covers ~/.emrg and anything nested under
     it) plus each explicit project path (covers projects outside ~/.emrg), and
     upserts every discovered session into ``config_root/sessions_index.json``.
+    Entries whose session directory no longer exists on disk are pruned (e.g.
+    sessions deleted out-of-band); entries pointing to live directories are
+    preserved even when the scan did not rediscover them.
     Returns the number of distinct sessions indexed.
     """
     index_path = config_root / _INDEX_FILENAME
@@ -177,5 +180,21 @@ def rebuild_sessions_index(
 
     for sid, sdir in found.items():
         data[sid] = sdir
+
+    # Prune stale entries whose session directory no longer exists on disk
+    # (removed out-of-band, outside the Session.delete hook). Rebuild stays a
+    # pure backfill for everything still alive — manual entries that point to a
+    # live directory are preserved.
+    stale = []
+    for sid, sdir in data.items():
+        try:
+            alive = Path(sdir).exists()
+        except (OSError, ValueError):
+            alive = False
+        if not alive:
+            stale.append(sid)
+    for sid in stale:
+        del data[sid]
+
     _write(data, index_path)
     return len(data)
diff --git a/tests/test_sessions_index.py b/tests/test_sessions_index.py
index 865e5bf..8798f00 100644
--- a/tests/test_sessions_index.py
+++ b/tests/test_sessions_index.py
@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import json
+import shutil
 from pathlib import Path
 
 from emrg.session import Session
@@ -138,16 +139,41 @@ def test_rebuild_skips_meta_without_sid(self, tmp_path):
         assert count == 0
 
     def test_rebuild_preserves_manual_entries(self, tmp_path):
+        """Manual entries pointing to a live directory survive the rebuild."""
         cfg = tmp_path / "cfg"
         cfg.mkdir(parents=True, exist_ok=True)
+        manual_dir = tmp_path / "manual_dir"
+        manual_dir.mkdir(parents=True, exist_ok=True)
         (cfg / "sessions_index.json").write_text(
-            json.dumps({"s_manual": "/tmp/manual"}), encoding="utf-8"
+            json.dumps({"s_manual": str(manual_dir)}), encoding="utf-8"
         )
         self._make_session(cfg, "s_scanned")
         count = rebuild_sessions_index(cfg)
         assert count == 2
         data = _load(cfg / "sessions_index.json")
-        assert data["s_manual"] == "/tmp/manual"
+        assert data["s_manual"] == str(manual_dir)
+        assert "s_scanned" in data
+
+    def test_rebuild_prunes_stale_entries(self, tmp_path):
+        """Index entries whose session dir was deleted out-of-band are dropped."""
+        cfg = tmp_path / "cfg"
+        cfg.mkdir(parents=True, exist_ok=True)
+        live_dir = tmp_path / "live"
+        live_dir.mkdir(parents=True, exist_ok=True)
+        dead_dir = tmp_path / "dead"
+        dead_dir.mkdir(parents=True, exist_ok=True)
+        (cfg / "sessions_index.json").write_text(
+            json.dumps({"s_live": str(live_dir), "s_dead": str(dead_dir)}),
+            encoding="utf-8",
+        )
+        # Delete the dead session's directory out-of-band (no Session.delete hook).
+        shutil.rmtree(dead_dir)
+        self._make_session(cfg, "s_scanned")
+        count = rebuild_sessions_index(cfg)
+        assert count == 2
+        data = _load(cfg / "sessions_index.json")
+        assert "s_dead" not in data
+        assert data["s_live"] == str(live_dir)
         assert "s_scanned" in data