diff --git a/cli.py b/cli.py
index b3e1c2fb8cb1..f4a1beb147f0 100644
--- a/cli.py
+++ b/cli.py
@@ -1927,10 +1927,15 @@ def _run_checkpoint_auto_maintenance() -> None:
         if not cfg.get("auto_prune", False):
             return
         from tools.checkpoint_manager import maybe_auto_prune_checkpoints
+        # delete_orphans is intentionally never honoured here: a missing
+        # workdir at startup is ambiguous (deleted project vs. an unmounted
+        # external volume / network share / VPN not yet up) and this sweep
+        # runs unattended. Orphan cleanup is only ever done via the explicit
+        # `hermes checkpoints prune` command, which the user has to invoke.
         maybe_auto_prune_checkpoints(
             retention_days=int(cfg.get("retention_days", 7)),
             min_interval_hours=int(cfg.get("min_interval_hours", 24)),
-            delete_orphans=bool(cfg.get("delete_orphans", True)),
+            delete_orphans=False,
             max_total_size_mb=int(cfg.get("max_total_size_mb", 500)),
         )
     except Exception as exc:
diff --git a/gateway/run.py b/gateway/run.py
index dbfc3326cd05..1c67ac3bc737 100644
--- a/gateway/run.py
+++ b/gateway/run.py
@@ -3415,18 +3415,24 @@ def __init__(self, config: Optional[GatewayConfig] = None):
             except Exception as exc:
                 logger.debug("state.db auto-maintenance skipped: %s", exc)
 
-        # Opportunistic shadow-repo cleanup — deletes orphan/stale
-        # checkpoint repos under ~/.hermes/checkpoints/.  Opt-in via
-        # checkpoints.auto_prune, idempotent via .last_prune marker.
+        # Opportunistic shadow-repo cleanup — deletes stale checkpoint repos
+        # under ~/.hermes/checkpoints/.  Opt-in via checkpoints.auto_prune,
+        # idempotent via .last_prune marker.
         try:
             from hermes_cli.config import load_config as _load_full_config
             _ckpt_cfg = (_load_full_config().get("checkpoints") or {})
             if _ckpt_cfg.get("auto_prune", False):
                 from tools.checkpoint_manager import maybe_auto_prune_checkpoints
+                # delete_orphans is intentionally never honoured here: a
+                # missing workdir at startup is ambiguous (deleted project
+                # vs. an unmounted external volume / network share / VPN
+                # not yet up) and this sweep runs unattended. Orphan cleanup
+                # is only ever done via the explicit `hermes checkpoints
+                # prune` command, which the user has to invoke.
                 maybe_auto_prune_checkpoints(
                     retention_days=int(_ckpt_cfg.get("retention_days", 7)),
                     min_interval_hours=int(_ckpt_cfg.get("min_interval_hours", 24)),
-                    delete_orphans=bool(_ckpt_cfg.get("delete_orphans", True)),
+                    delete_orphans=False,
                     max_total_size_mb=int(_ckpt_cfg.get("max_total_size_mb", 500)),
                 )
         except Exception as exc:
diff --git a/hermes_cli/checkpoints.py b/hermes_cli/checkpoints.py
index 2975553ae495..a5cdbe6daed3 100644
--- a/hermes_cli/checkpoints.py
+++ b/hermes_cli/checkpoints.py
@@ -109,20 +109,49 @@ def cmd_list(args: argparse.Namespace) -> int:
 
 
 def cmd_prune(args: argparse.Namespace) -> int:
-    from tools.checkpoint_manager import prune_checkpoints
+    from tools.checkpoint_manager import prune_checkpoints, store_status
 
     retention_days = args.retention_days
     max_size_mb = args.max_size_mb
+    delete_orphans = not args.keep_orphans
+
+    if delete_orphans and not args.force:
+        info = store_status()
+        orphans = [
+            p for p in info.get("projects", [])
+            if not p.get("exists")
+        ]
+        pre_v2_orphans = [
+            p for p in info.get("pre_v2_projects", [])
+            if not p.get("exists")
+        ]
+        if orphans or pre_v2_orphans:
+            print(f"This will permanently delete {len(orphans) + len(pre_v2_orphans)} "
+                  "orphan checkpoint project(s) whose workdir is not currently reachable:")
+            print()
+            for p in orphans:
+                wd = p.get("workdir") or "(unknown)"
+                print(f"  {wd}  ({p.get('commits', 0)} commit(s))")
+            for p in pre_v2_orphans:
+                wd = p.get("workdir") or "(unknown)"
+                print(f"  {wd}  (pre-v2 shadow repo)")
+            print()
+            print("A workdir can be unreachable because the project was deleted,")
+            print("or because an external volume / network share / VPN is down.")
+            print("Pass --keep-orphans to prune stale entries only.")
+            if not _confirm("Delete these orphan projects?"):
+                print("Aborted.")
+                return 1
 
     print("Pruning checkpoint store…")
     print(f"  retention_days:    {retention_days}")
-    print(f"  delete_orphans:    {not args.keep_orphans}")
+    print(f"  delete_orphans:    {delete_orphans}")
     print(f"  max_total_size_mb: {max_size_mb}")
     print()
 
     result = prune_checkpoints(
         retention_days=retention_days,
-        delete_orphans=not args.keep_orphans,
+        delete_orphans=delete_orphans,
         max_total_size_mb=max_size_mb,
     )
     print(f"Scanned:         {result['scanned']}")
@@ -225,6 +254,8 @@ def register_cli(parser: argparse.ArgumentParser) -> None:
                               "per project until total size <= this (default 500)")
     p_prune.add_argument("--keep-orphans", action="store_true",
                          help="Skip deleting projects whose workdir no longer exists")
+    p_prune.add_argument("-f", "--force", action="store_true",
+                         help="Skip the orphan-deletion confirmation prompt")
     p_prune.set_defaults(func=cmd_prune)
 
     p_clear = subs.add_parser(
diff --git a/hermes_cli/config.py b/hermes_cli/config.py
index 23c1b7c66e31..4203bd27c01a 100644
--- a/hermes_cli/config.py
+++ b/hermes_cli/config.py
@@ -1369,15 +1369,22 @@ def _ensure_hermes_home_managed(home: Path):
         "max_file_size_mb": 10,
         # Auto-maintenance: hermes sweeps the checkpoint base at startup
         # (at most once per ``min_interval_hours``) and:
-        #   * deletes project entries whose workdir no longer exists (orphan)
         #   * deletes project entries whose last_touch is older than
         #     ``retention_days``
         #   * GCs the single shared store to reclaim unreachable objects
         #   * enforces ``max_total_size_mb`` across remaining projects
         #   * deletes ``legacy-*`` archives older than ``retention_days``
+        #
+        # NOTE: this automatic sweep never deletes "orphan" entries (workdir
+        # no longer found on disk). A missing workdir at startup is
+        # ambiguous — it can mean the project was deleted, or that an
+        # external volume / network share / VPN is simply not mounted yet —
+        # and this sweep runs unattended, so it must never guess. Orphan
+        # cleanup is only available via the explicit
+        # ``hermes checkpoints prune`` command (add ``--keep-orphans`` to
+        # skip it), where a human is looking at the output.
         "auto_prune": True,
         "retention_days": 7,
-        "delete_orphans": True,
         "min_interval_hours": 24,
     },
 
diff --git a/tests/hermes_cli/test_checkpoints_prune.py b/tests/hermes_cli/test_checkpoints_prune.py
new file mode 100644
index 000000000000..d597bc86f9c2
--- /dev/null
+++ b/tests/hermes_cli/test_checkpoints_prune.py
@@ -0,0 +1,208 @@
+"""Tests for `hermes checkpoints prune`'s orphan confirmation flow.
+
+Covers the P1 raised on PR #69141: the confirmation preview must cover
+BOTH v2 projects (`store_status()["projects"]`) and pre-v2 shadow repos
+(`store_status()["pre_v2_projects"]`), since `prune_checkpoints()` deletes
+orphans from both layouts. Exercises decline / accept / --force across
+pre-v2-only and mixed (v2 + pre-v2) stores.
+"""
+
+from __future__ import annotations
+
+import argparse
+
+import pytest
+
+
+def _ns(**kwargs) -> argparse.Namespace:
+    defaults = {"retention_days": 7, "max_size_mb": 500, "keep_orphans": False, "force": False}
+    defaults.update(kwargs)
+    return argparse.Namespace(**defaults)
+
+
+def _prune_result(**kwargs) -> dict:
+    result = {"scanned": 0, "deleted_orphan": 0, "deleted_stale": 0, "errors": 0, "bytes_freed": 0}
+    result.update(kwargs)
+    return result
+
+
+_V2_ORPHAN_ONLY_STATUS = {
+    "projects": [],
+    "pre_v2_projects": [],
+}
+
+_PRE_V2_ONLY_STATUS = {
+    "projects": [],
+    "pre_v2_projects": [
+        {"path": "/home/user/.hermes/checkpoints/deadbeefcafebabe", "workdir": None, "exists": False},
+    ],
+}
+
+_MIXED_STATUS = {
+    "projects": [
+        {"hash": "abc123", "workdir": "/gone/v2-project", "exists": False, "commits": 4},
+    ],
+    "pre_v2_projects": [
+        {"path": "/home/user/.hermes/checkpoints/deadbeefcafebabe", "workdir": "/gone/pre-v2-project", "exists": False},
+    ],
+}
+
+
+def _patch_checkpoint_manager(monkeypatch, status: dict, prune_calls: list):
+    import tools.checkpoint_manager as ckpt_mgr
+
+    monkeypatch.setattr(ckpt_mgr, "store_status", lambda *a, **k: status)
+
+    def _fake_prune(**kwargs):
+        prune_calls.append(kwargs)
+        return _prune_result(
+            deleted_orphan=len(status["projects"]) + len(status["pre_v2_projects"]),
+        )
+
+    monkeypatch.setattr(ckpt_mgr, "prune_checkpoints", _fake_prune)
+
+
+# ─── pre-v2-only store ──────────────────────────────────────────────────────
+
+
+def test_pre_v2_only_decline_aborts_without_deleting(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _PRE_V2_ONLY_STATUS, prune_calls)
+    monkeypatch.setattr("builtins.input", lambda _prompt: "n")
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 1
+    assert prune_calls == []
+    out = capsys.readouterr().out
+    assert "pre-v2 shadow repo" in out
+    assert "Aborted" in out
+
+
+def test_pre_v2_only_accept_deletes(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _PRE_V2_ONLY_STATUS, prune_calls)
+    monkeypatch.setattr("builtins.input", lambda _prompt: "y")
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+    assert prune_calls[0]["delete_orphans"] is True
+
+
+def test_pre_v2_only_force_skips_prompt(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _PRE_V2_ONLY_STATUS, prune_calls)
+
+    def _unexpected_input(_prompt):
+        raise AssertionError("input() must not be called when --force is passed")
+
+    monkeypatch.setattr("builtins.input", _unexpected_input)
+
+    rc = checkpoints_cli.cmd_prune(_ns(force=True))
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+
+
+# ─── mixed store (v2 + pre-v2) ──────────────────────────────────────────────
+
+
+def test_mixed_store_decline_aborts_without_deleting(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _MIXED_STATUS, prune_calls)
+    monkeypatch.setattr("builtins.input", lambda _prompt: "n")
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 1
+    assert prune_calls == []
+    out = capsys.readouterr().out
+    # Both layouts must appear in the preview, not just the v2 one.
+    assert "/gone/v2-project" in out
+    assert "/gone/pre-v2-project" in out
+    assert "This will permanently delete 2 orphan checkpoint project(s)" in out
+
+
+def test_mixed_store_accept_deletes_both_layouts(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _MIXED_STATUS, prune_calls)
+    monkeypatch.setattr("builtins.input", lambda _prompt: "y")
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+    out = capsys.readouterr().out
+    assert "Deleted orphan:  2" in out
+
+
+def test_mixed_store_force_skips_prompt_deletes_both(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _MIXED_STATUS, prune_calls)
+
+    def _unexpected_input(_prompt):
+        raise AssertionError("input() must not be called when --force is passed")
+
+    monkeypatch.setattr("builtins.input", _unexpected_input)
+
+    rc = checkpoints_cli.cmd_prune(_ns(force=True))
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+    assert prune_calls[0]["delete_orphans"] is True
+
+
+# ─── --keep-orphans skips the prompt entirely, on either layout ───────────
+
+
+@pytest.mark.parametrize("status", [_PRE_V2_ONLY_STATUS, _MIXED_STATUS], ids=["pre_v2_only", "mixed"])
+def test_keep_orphans_skips_prompt(monkeypatch, capsys, status):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, status, prune_calls)
+
+    def _unexpected_input(_prompt):
+        raise AssertionError("input() must not be called when --keep-orphans is passed")
+
+    monkeypatch.setattr("builtins.input", _unexpected_input)
+
+    rc = checkpoints_cli.cmd_prune(_ns(keep_orphans=True))
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+    assert prune_calls[0]["delete_orphans"] is False
+
+
+# ─── no orphans present: never prompts even without --force ───────────────
+
+
+def test_no_orphans_skips_prompt(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _V2_ORPHAN_ONLY_STATUS, prune_calls)
+
+    def _unexpected_input(_prompt):
+        raise AssertionError("input() must not be called when there are no orphans")
+
+    monkeypatch.setattr("builtins.input", _unexpected_input)
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 0
+    assert len(prune_calls) == 1
diff --git a/tools/checkpoint_manager.py b/tools/checkpoint_manager.py
index b5ce04c6a64e..919655d3c8d7 100644
--- a/tools/checkpoint_manager.py
+++ b/tools/checkpoint_manager.py
@@ -545,6 +545,39 @@ def _list_projects(store: Path) -> List[Dict]:
     return out
 
 
+def _pre_v2_shadow_repos(base: Path) -> List[Dict]:
+    """Return pre-v2 per-project shadow repos still directly under ``base``.
+
+    Pre-v2 layout kept one shadow git repo per working directory directly
+    under ``CHECKPOINT_BASE`` (identified by a ``HEAD`` file).  This is the
+    single source of truth for that scan so a preview built from it (e.g.
+    ``store_status``) always matches what ``prune_checkpoints`` deletes.
+    """
+    out: List[Dict] = []
+    if not base.exists():
+        return out
+    for child in base.iterdir():
+        if not child.is_dir():
+            continue
+        if child.name == _STORE_DIRNAME or child.name.startswith(_LEGACY_PREFIX):
+            continue
+        if not (child / "HEAD").exists():
+            continue
+        workdir: Optional[str] = None
+        wd_marker = child / "HERMES_WORKDIR"
+        if wd_marker.exists():
+            try:
+                workdir = wd_marker.read_text(encoding="utf-8").strip()
+            except (OSError, UnicodeDecodeError):
+                workdir = None
+        out.append({
+            "path": child,
+            "workdir": workdir,
+            "exists": bool(workdir) and Path(workdir).exists(),
+        })
+    return out
+
+
 def _dir_file_count(path: str) -> int:
     """Quick file count estimate (stops early if over _MAX_FILES)."""
     count = 0
@@ -1325,22 +1358,16 @@ def prune_checkpoints(
             except OSError as exc:
                 result["errors"] += 1
                 logger.warning("Failed to delete legacy archive %s: %s", child, exc)
-            continue
-        # Only count as a pre-v2 shadow repo if it has a HEAD.
-        if not (child / "HEAD").exists():
-            continue
+
+    # Pre-v2 per-project shadow repos.  Scanned via the same helper
+    # `store_status()` uses for its orphan preview, so a confirmation prompt
+    # built from that preview always matches what gets deleted here.
+    for repo in _pre_v2_shadow_repos(base):
+        child = repo["path"]
         result["scanned"] += 1
         reason: Optional[str] = None
-        if delete_orphans:
-            workdir: Optional[str] = None
-            wd_marker = child / "HERMES_WORKDIR"
-            if wd_marker.exists():
-                try:
-                    workdir = wd_marker.read_text(encoding="utf-8").strip()
-                except (OSError, UnicodeDecodeError):
-                    workdir = None
-            if workdir is None or not Path(workdir).exists():
-                reason = "orphan"
+        if delete_orphans and not repo["exists"]:
+            reason = "orphan"
         if reason is None and retention_days > 0:
             newest = 0.0
             try:
@@ -1572,7 +1599,14 @@ def store_status(checkpoint_base: Optional[Path] = None) -> Dict:
 
     ``{"base": path, "store_size_bytes": N, "legacy_size_bytes": N,
        "total_size_bytes": N, "project_count": N, "projects": [...],
-       "legacy_archives": [...]}``
+       "pre_v2_projects": [...], "legacy_archives": [...]}``
+
+    ``pre_v2_projects`` covers shadow repos still on the pre-v2 per-project
+    layout (``base/<hash>/HEAD``) — distinct from ``legacy_archives``, which
+    are already-migrated ``legacy-<ts>/`` dirs. Callers that preview an
+    orphan-deletion sweep must include both ``projects`` and
+    ``pre_v2_projects``, since ``prune_checkpoints`` deletes orphans from
+    both layouts.
     """
     base = checkpoint_base or CHECKPOINT_BASE
     out: Dict = {
@@ -1582,6 +1616,7 @@ def store_status(checkpoint_base: Optional[Path] = None) -> Dict:
         "total_size_bytes": 0,
         "project_count": 0,
         "projects": [],
+        "pre_v2_projects": [],
         "legacy_archives": [],
     }
     if not base.exists():
@@ -1613,6 +1648,15 @@ def store_status(checkpoint_base: Optional[Path] = None) -> Dict:
                 })
     out["project_count"] = len(out["projects"])
 
+    out["pre_v2_projects"] = [
+        {
+            "path": str(r["path"]),
+            "workdir": r["workdir"],
+            "exists": r["exists"],
+        }
+        for r in _pre_v2_shadow_repos(base)
+    ]
+
     for child in base.iterdir():
         if child.is_dir() and child.name.startswith(_LEGACY_PREFIX):
             try:
diff --git a/website/docs/user-guide/checkpoints-and-rollback.md b/website/docs/user-guide/checkpoints-and-rollback.md
index 1393060612e2..a71ec2fe5b79 100644
--- a/website/docs/user-guide/checkpoints-and-rollback.md
+++ b/website/docs/user-guide/checkpoints-and-rollback.md
@@ -94,12 +94,15 @@ checkpoints:
   max_file_size_mb: 10        # skip any single file larger than this
 
   # Auto-maintenance (on by default): sweep ~/.hermes/checkpoints/ at startup
-  # and delete project entries whose working directory no longer exists
-  # (orphans) or whose last_touch is older than retention_days. Runs at most
-  # once per min_interval_hours, tracked via a .last_prune marker.
+  # and delete project entries whose last_touch is older than retention_days.
+  # Runs at most once per min_interval_hours, tracked via a .last_prune
+  # marker. This sweep never deletes "orphan" entries (working directory not
+  # found) — a missing workdir at startup is ambiguous (deleted project vs.
+  # an unmounted external volume / network share / VPN not yet up), so
+  # orphan cleanup is only ever done via the explicit
+  # `hermes checkpoints prune` command below, with a confirmation prompt.
   auto_prune: true
   retention_days: 7
-  delete_orphans: true
   min_interval_hours: 24
 ```
 
diff --git a/website/i18n/zh-Hans/docusaurus-plugin-content-docs/current/user-guide/checkpoints-and-rollback.md b/website/i18n/zh-Hans/docusaurus-plugin-content-docs/current/user-guide/checkpoints-and-rollback.md
index 472b30f930ab..dec3ddb259d9 100644
--- a/website/i18n/zh-Hans/docusaurus-plugin-content-docs/current/user-guide/checkpoints-and-rollback.md
+++ b/website/i18n/zh-Hans/docusaurus-plugin-content-docs/current/user-guide/checkpoints-and-rollback.md
@@ -94,12 +94,14 @@ checkpoints:
   max_file_size_mb: 10        # 跳过大于此值的单个文件
 
   # 自动维护（默认开启）：启动时扫描 ~/.hermes/checkpoints/，
-  # 删除工作目录已不存在的项目条目（孤立项）或 last_touch 超过
-  # retention_days 的条目。通过 .last_prune 标记控制，
-  # 最多每 min_interval_hours 运行一次。
+  # 删除 last_touch 超过 retention_days 的条目。通过 .last_prune
+  # 标记控制，最多每 min_interval_hours 运行一次。此扫描不会删除
+  # “孤立”条目（工作目录未找到）——启动时工作目录缺失含义模糊
+  # （项目被删除，还是外部卷/网络共享/VPN 尚未挂载），因此孤立项
+  # 清理只能通过下方的 `hermes checkpoints prune` 命令显式触发，
+  # 并会要求确认。
   auto_prune: true
   retention_days: 7
-  delete_orphans: true
   min_interval_hours: 24
 ```