diff --git a/CHANGELOG.md b/CHANGELOG.md
index 82960dc779..9058e0e135 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+
+- `apm install -g` into one Claude profile (`CLAUDE_CONFIG_DIR`) or Hermes home (`HERMES_HOME`) no longer deletes files deployed to another profile through the shared user lockfile; stale-file cleanup is limited to the selected root. (#3423)
+
 ## [0.35.0] - 2026-10-22
 
 ### Added
diff --git a/docs/src/content/docs/integrations/hermes.md b/docs/src/content/docs/integrations/hermes.md
index 8b9603f196..46597370f9 100644
--- a/docs/src/content/docs/integrations/hermes.md
+++ b/docs/src/content/docs/integrations/hermes.md
@@ -47,7 +47,7 @@ export HERMES_HOME="$HOME/.config/hermes"
 apm install --target hermes --global
 ```
 
-When `HERMES_HOME` lives under `$HOME`, APM keeps the deploy root home-relative; otherwise it uses the absolute path. The directory does not need to exist yet.
+When `HERMES_HOME` lives under `$HOME`, APM keeps the deploy root home-relative; otherwise it uses the absolute path. The directory does not need to exist yet. Hermes homes share one user lockfile; a global install removes stale skills only under the selected `HERMES_HOME`, leaving skills deployed to other homes in place.
 
 ## MCP servers
 
diff --git a/docs/src/content/docs/reference/cli/install.md b/docs/src/content/docs/reference/cli/install.md
index 909e7d016e..ab2253c402 100644
--- a/docs/src/content/docs/reference/cli/install.md
+++ b/docs/src/content/docs/reference/cli/install.md
@@ -208,7 +208,7 @@ still cleans up its managed files, subject to the usual user-edit protections.
 - **Direct registry lookup fails closed.** Registry-form MCP entries (`apm install --mcp NAME` with no `--url` and no post-`--` command) resolve one unique registry identity before writing the manifest or user config. An unreachable registry, missing identity, or ambiguous bare server name exits non-zero without changing state.
 - **Diff-aware.** Packages whose ref or version changed in `apm.yml` are re-downloaded automatically. MCP servers with matching config are skipped; unchanged APM-managed connections can be updated when their declaration changes.
 - **Claude/Codex MCP collisions.** A differing self-defined connection with the same name is preserved unless its native configuration still matches the recorded APM baseline. Install identifies the conflicting target and exits nonzero; successful writes to other targets remain recorded. An identical foreign entry is not adopted. Neither `--force` nor `--frozen` takes over a user connection. Removal also preserves entries with a differing or unverifiable baseline. See [MCP conflict recovery](../../../consumer/install-mcp-servers/#resolve-a-connection-name-conflict).
-- **Claude Code profiles.** For user-scope MCP installs, an absolute `CLAUDE_CONFIG_DIR` selects that profile's `.claude.json` for both installation and stale-server cleanup. Removing an APM-managed server in the selected profile preserves other profiles and user-owned entries. Cleanup refuses symlinked config files or profile directories; replace the link with a regular file or directory before retrying.
+- **Claude Code profiles.** For user-scope MCP installs, an absolute `CLAUDE_CONFIG_DIR` selects that profile's `.claude.json` for both installation and stale-server cleanup. Removing an APM-managed server in the selected profile preserves other profiles and user-owned entries. Cleanup refuses symlinked config files or profile directories; replace the link with a regular file or directory before retrying. Skills, agents, and other deployed files follow the same rule: profiles share one user lockfile, and a global install removes stale files only under the selected `CLAUDE_CONFIG_DIR` (or `~/.claude`), leaving files deployed to other profiles in place. Files of a profile you no longer install into stay on disk and in the lockfile; remove them manually.
 - **Transactional replacement.** `--update` and `--refresh` download package
   replacements to isolated staging paths and validate them before publication.
   Failed downloads or validation leave the previous package active. Failed
diff --git a/src/apm_cli/core/deployment_state.py b/src/apm_cli/core/deployment_state.py
index 6333f18e0f..c6bf761379 100644
--- a/src/apm_cli/core/deployment_state.py
+++ b/src/apm_cli/core/deployment_state.py
@@ -525,11 +525,20 @@ def _filter_absent_owners(
         )
 
     def _is_stale(self, record: DeploymentRecord, intent: DeploymentIntent) -> bool:
+        """Decide whether an unrefreshed row lost its target this run.
+
+        A row of an active target is stale unless it lies under another
+        profile root of that target (``CLAUDE_CONFIG_DIR``, ``HERMES_HOME``).
+        A row of a known target dropped from the declared set is stale too.
+        """
         if not intent.authoritative_targets:
             return False
         target = record.locator.target
         if target in intent.active_targets:
-            return True
+            from apm_cli.integration.targets import is_other_profile_path
+
+            profile = self.target_profiles.get(target)
+            return profile is None or not is_other_profile_path(profile, record.locator.value)
         return (
             intent.declared_targets is not None
             and target in self.target_profiles
diff --git a/src/apm_cli/integration/targets.py b/src/apm_cli/integration/targets.py
index 1c4fa98d18..3a20c28b74 100644
--- a/src/apm_cli/integration/targets.py
+++ b/src/apm_cli/integration/targets.py
@@ -53,6 +53,16 @@
 on the mapping, and add a ``_convert_to_*`` branch in ``_render_instruction``.
 """
 
+USER_ROOT_ENV_VARS: dict[str, str] = {
+    "claude": "CLAUDE_CONFIG_DIR",
+    "hermes": "HERMES_HOME",
+}
+"""Targets whose user-scope root an environment variable selects.
+
+Each value of the variable is a separate profile of the same runtime, and
+all of them share one user lockfile.
+"""
+
 
 @dataclass(frozen=True)
 class PrimitiveMapping:
@@ -475,12 +485,11 @@ def for_scope(self, user_scope: bool = False) -> TargetProfile | None:
         # Claude Code honors CLAUDE_CONFIG_DIR (default ~/.claude) and Hermes
         # honors HERMES_HOME (default ~/.hermes); mirror that at user scope so
         # `apm install -g` lands where the tool reads.
-        if self.name in ("claude", "hermes"):
+        if self.name in USER_ROOT_ENV_VARS:
             import os
             from pathlib import Path
 
-            env_var = "CLAUDE_CONFIG_DIR" if self.name == "claude" else "HERMES_HOME"
-            env = os.environ.get(env_var, "").strip()
+            env = os.environ.get(USER_ROOT_ENV_VARS[self.name], "").strip()
             if env:
                 # ``resolve`` collapses ``..`` so traversal segments cannot
                 # leak into ``root_dir`` and escape ``project_root / root_dir``.
@@ -1272,6 +1281,25 @@ def get_integration_prefixes(targets=None, *, user_scope: bool = False) -> tuple
     return tuple(prefixes)
 
 
+def is_other_profile_path(profile: TargetProfile, value: str) -> bool:
+    """Return True when *value* was deployed to another profile of *profile*.
+
+    Profiles of a target listed in :data:`USER_ROOT_ENV_VARS` share one user
+    lockfile, so its ``deployed_files`` can list paths under the roots of
+    profiles other than the selected one.  Such a path is not stale for an
+    install into the selected profile.  The check is a lexical prefix match
+    against the selected root; it neither resolves nor follows symlinks.
+    Separators are compared in POSIX form: an absolute root keeps native
+    separators (``D:\\profiles\\b``) while lockfile values use ``/``.
+    """
+    if profile.name not in USER_ROOT_ENV_VARS or "://" in value:
+        return False
+    prefixes = tuple(
+        prefix.replace("\\", "/") for prefix in get_integration_prefixes(targets=[profile])
+    )
+    return not value.replace("\\", "/").startswith(prefixes)
+
+
 def active_targets_user_scope(
     explicit_target: str | list[str] | None = None,
     *,
diff --git a/tests/integration/test_claude_config_profile_lifecycle.py b/tests/integration/test_claude_config_profile_lifecycle.py
index 54583a33eb..a305ed648d 100644
--- a/tests/integration/test_claude_config_profile_lifecycle.py
+++ b/tests/integration/test_claude_config_profile_lifecycle.py
@@ -165,3 +165,64 @@ def test_claude_profile_cleanup_refuses_unsafe_paths_without_changing_state(
     )
     assert config.read_bytes() == config_before
     assert lock_path.read_bytes() == lock_before
+
+
+def _skills(root: Path) -> set[str]:
+    """Return the names of skills deployed under one Claude profile root."""
+    return {path.parent.name for path in (root / "skills").glob("*/SKILL.md")}
+
+
+@pytest.mark.parametrize("location", ["home", "outside-home"])
+def test_claude_profile_install_keeps_files_deployed_to_other_profiles(
+    tmp_path: Path, location: str
+) -> None:
+    """A -> B -> A -> B keeps both profiles; stale cleanup stays in the selected one (#3423)."""
+    isolated, cwd, runner = _scenario(tmp_path)
+    dump_yaml({"name": "skills-home", "version": "0.1.0"}, isolated.config_root / "apm.yml")
+    factory = LocalPackageFactory(isolated.package_root)
+    package = factory.create("profile-skills", targets=("claude",))
+    factory.add_skill(package, "keep", "---\nname: keep\ndescription: Kept.\n---\nKeep.\n")
+    renamed = factory.add_skill(
+        package, "renamed", "---\nname: renamed\ndescription: Removed.\n---\nRemoved.\n"
+    )
+    default = isolated.home / ".claude"
+    profile_b = (isolated.home if location == "home" else isolated.root) / "profiles" / "b"
+    lock_path = isolated.config_root / "apm.lock.yaml"
+    all_skills = {"keep", "renamed"}
+
+    def install(root: Path) -> None:
+        """Install the local package into the profile rooted at *root*."""
+        result = runner.run(
+            ("install", "--global", str(package.root), "--target", "claude", "--no-policy"),
+            scenario_id="claude-profile-files",
+            cwd=cwd,
+            env={
+                **isolated.subprocess_env(),
+                "CLAUDE_CONFIG_DIR": "" if root == default else str(root),
+            },
+        )
+        assert result.returncode == 0, result.stdout + result.stderr
+
+    install(default)
+    assert _skills(default) == all_skills
+    for root in (profile_b, default, profile_b):
+        install(root)
+        assert _skills(default) == all_skills
+        assert _skills(profile_b) == all_skills
+
+    lock_before = lock_path.read_bytes()
+    install(profile_b)
+    assert lock_path.read_bytes() == lock_before
+    assert _skills(default) == all_skills
+    assert _skills(profile_b) == all_skills
+
+    # A skill dropped from the package is removed only from the selected
+    # profile; the other profile is cleaned when it is installed into.
+    renamed.unlink()
+    renamed.parent.rmdir()
+    install(profile_b)
+    assert _skills(profile_b) == {"keep"}
+    assert _skills(default) == all_skills
+    install(default)
+    assert _skills(default) == {"keep"}
+    assert _skills(profile_b) == {"keep"}
diff --git a/tests/unit/core/test_deployment_state.py b/tests/unit/core/test_deployment_state.py
index 79f750f79f..4641337c49 100644
--- a/tests/unit/core/test_deployment_state.py
+++ b/tests/unit/core/test_deployment_state.py
@@ -420,6 +420,38 @@ def test_same_target_stale_and_undeclared_target_are_removed(tmp_path: Path) ->
     assert set(reconciled.removed) == {active, ghost}
 
 
+@pytest.mark.parametrize(
+    ("selected_root", "selected_value"),
+    [
+        ("profiles/b", "profiles/b"),
+        ("/outside/profiles/b", "/outside/profiles/b"),
+        ("D:\\profiles\\b", "D:/profiles/b"),
+    ],
+    ids=["home-relative", "absolute", "windows-absolute"],
+)
+@pytest.mark.parametrize(("target", "default_root"), [("claude", ".claude"), ("hermes", ".hermes")])
+def test_other_profile_rows_are_not_stale(
+    tmp_path: Path, selected_root: str, selected_value: str, target: str, default_root: str
+) -> None:
+    """Rows under another CLAUDE_CONFIG_DIR/HERMES_HOME root survive an install into the selected one."""
+    selected = _locator(f"{selected_value}/skills/demo/SKILL.md", target=target)
+    default = _locator(f"{default_root}/skills/demo/SKILL.md", target=target)
+    sibling = _locator("profiles/c/skills/demo/SKILL.md", target=target)
+    prior = DeploymentLedger(
+        records={locator.key: _record(locator) for locator in (selected, default, sibling)}
+    )
+    reconciler = DeploymentReconciler(
+        tmp_path,
+        {target: _target(target, selected_root)},
+        diagnostics=DiagnosticCollector(),
+    )
+
+    reconciled = reconciler.reconcile(prior, [], _intent(active=frozenset({target})))
+
+    assert reconciled.removed == (selected,)
+    assert set(reconciled.ledger.records) == {default.key, sibling.key}
+
+
 @pytest.mark.parametrize(
     ("dropped_target", "surviving_target"),
     (