diff --git a/src/specify_cli/integrations/_file_changes.py b/src/specify_cli/integrations/_file_changes.py
index 9ed0ebc62f..dd9878bee3 100644
--- a/src/specify_cli/integrations/_file_changes.py
+++ b/src/specify_cli/integrations/_file_changes.py
@@ -45,3 +45,10 @@ def write_bytes(path: Path, content: bytes) -> int:
 def unlink(path: Path, *, missing_ok: bool = False) -> None:
     with changing_file(path, removal=True):
         path.unlink(missing_ok=missing_ok)
+
+
+def rmdir(path: Path) -> None:
+    """Journal and remove an empty directory without snapshotting user files."""
+    if not any(path.iterdir()):
+        with changing_file(path, removal=True):
+            path.rmdir()
diff --git a/src/specify_cli/presets/_manager_skills.py b/src/specify_cli/presets/_manager_skills.py
index 5a4a4fb739..18baf05b4b 100644
--- a/src/specify_cli/presets/_manager_skills.py
+++ b/src/specify_cli/presets/_manager_skills.py
@@ -2,7 +2,6 @@
 
 import copy
 import os
-import shutil
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Set, Union
 
@@ -216,7 +215,7 @@ def apply_to_dir(
                 managed_skill_names if managed_names is None else managed_names
             )
             # Restore skills for commands whose winner is non-preset.
-            # _unregister_skills_in_dir can rmtree the skill dir, so
+            # _unregister_skills_in_dir can remove the skill file, so
             # overrides must be handled directly (create dir + write)
             # without that call.
             dir_core_ext_names = [
@@ -1275,11 +1274,13 @@ def _delete_agent_preset_skills(
             if override_source:
                 owned_sources.add(override_source)
             if source in owned_sources:
-                from ..integrations._file_changes import after_file_change, before_file_change
+                from ..integrations._file_changes import rmdir, unlink
 
-                before_file_change(skill_subdir, removal=True)
-                shutil.rmtree(skill_subdir)
-                after_file_change(skill_subdir)
+                unlink(skill_file)
+                try:
+                    rmdir(skill_subdir)
+                except OSError:
+                    pass
 
     @staticmethod
     def _warn_unrestored_skill(
@@ -1370,7 +1371,7 @@ def _unregister_skills_in_dir(
             # is_dir() follows symlinks, so a symlinked skill subdirectory
             # (with a safe, non-symlinked parent) would otherwise slip past
             # _safe_skills_dir_for_agent's parent-only check and have
-            # write_text/rmtree operate through it (#2948).
+            # writes/removals operate through it (#2948).
             if not self._validate_skill_subdir(
                 skill_subdir, create=False, skills_root=skills_dir
             ):
@@ -1435,7 +1436,7 @@ def _unregister_skills_in_dir(
                 # source cannot produce restored content, so leave the
                 # existing skill untouched rather than leaking a raw
                 # OSError/UnicodeDecodeError out of `preset remove` — and
-                # rather than falling through to the rmtree below, which
+                # rather than falling through to the removal below, which
                 # would delete a skill precisely when its replacement
                 # cannot be generated. Matches the `continue` guards above
                 # (unsafe name, missing subdir, foreign owner), which also
@@ -1541,12 +1542,14 @@ def _unregister_skills_in_dir(
                 _write_shared_text(skills_dir, skill_file, skill_content)
                 mutated_names.append(skill_name)
             else:
-                # No core or extension template — remove the skill entirely
-                from ..integrations._file_changes import after_file_change, before_file_change
+                # No core or extension template — remove only the generated file
+                from ..integrations._file_changes import rmdir, unlink
 
-                before_file_change(skill_subdir, removal=True)
-                shutil.rmtree(skill_subdir)
-                after_file_change(skill_subdir)
+                unlink(skill_file)
+                try:
+                    rmdir(skill_subdir)
+                except OSError:
+                    pass
                 mutated_names.append(skill_name)
 
         return mutated_names
diff --git a/tests/specify_cli/presets/test_command_remove.py b/tests/specify_cli/presets/test_command_remove.py
index 50a7e89f7b..dddb395248 100644
--- a/tests/specify_cli/presets/test_command_remove.py
+++ b/tests/specify_cli/presets/test_command_remove.py
@@ -2,9 +2,12 @@
 
 from __future__ import annotations
 
+import os
+import stat
 from pathlib import Path
 from unittest.mock import patch
 
+import pytest
 from typer.testing import CliRunner
 
 from specify_cli import app
@@ -19,3 +22,101 @@ def test_remove_installed_preset(project_dir, pack_dir):
 
     assert result.exit_code == 0, result.output
     assert not PresetManager(project_dir).registry.is_installed("test-pack")
+
+
+@pytest.mark.parametrize("operation", ["remove", "switch"])
+@pytest.mark.parametrize("user_reference", [False, True])
+def test_preset_skill_cleanup_preserves_user_files(tmp_path, monkeypatch, operation, user_reference):
+    monkeypatch.chdir(tmp_path)
+    runner = CliRunner()
+    preset = Path(__file__).resolve().parents[3] / "presets" / "scaffold"
+    for args in (
+        ["init", "--here", "--integration", "copilot", "--script", "sh", "--ignore-agent-tools"],
+        ["preset", "add", "--dev", str(preset)],
+    ):
+        result = runner.invoke(app, args, catch_exceptions=False)
+        assert result.exit_code == 0, result.output
+    skill_dir = tmp_path / ".github/skills/speckit-myext-myextcmd"
+    reference = skill_dir / "references" / "user.md"
+    original = b"\xef\xbb\xbf# User reference\r\nKeep my project notes."
+    if user_reference:
+        reference.parent.mkdir()
+        reference.write_bytes(original)
+
+    args = ["preset", "remove", "my-preset"] if operation == "remove" else ["integration", "switch", "claude"]
+    result = runner.invoke(app, args, catch_exceptions=False)
+
+    assert result.exit_code == 0, result.output
+    assert not (skill_dir / "SKILL.md").exists()
+    if user_reference:
+        assert reference.is_file()
+        assert reference.read_bytes() == original
+    else:
+        assert not skill_dir.exists()
+
+
+@pytest.mark.parametrize("operation", ["remove", "switch"])
+@pytest.mark.parametrize("user_reference", [False, True])
+def test_preset_skill_cleanup_rollback_preserves_directory_mode(
+    tmp_path, monkeypatch, capsys, operation, user_reference,
+):
+    from specify_cli.integrations._helpers import _read_integration_json
+    from specify_cli.integrations._lifecycle import _FileJournal, _transaction
+    from specify_cli.integrations.installer import read_records
+
+    project = tmp_path / "project"
+    project.mkdir()
+    (tmp_path / "home").mkdir()
+    monkeypatch.chdir(project)
+    monkeypatch.setenv("HOME", str(tmp_path / "home"))
+    monkeypatch.setenv("USERPROFILE", str(tmp_path / "home"))
+    runner = CliRunner()
+    preset = Path(__file__).resolve().parents[3] / "presets" / "scaffold"
+    for args in (
+        ["init", "--here", "--integration", "copilot", "--script", "sh", "--ignore-agent-tools"],
+        ["preset", "add", "--dev", str(preset)],
+    ):
+        result = runner.invoke(app, args, catch_exceptions=False)
+        assert result.exit_code == 0, result.output
+    skill_dir = project / ".github/skills/speckit-myext-myextcmd"
+    skill_file = skill_dir / "SKILL.md"
+    original = skill_file.read_bytes()
+    skill_dir.chmod(0o700)
+    reference = skill_dir / "references/user.md"
+    if user_reference:
+        reference.parent.mkdir()
+        reference.write_bytes(b"User reference before cleanup")
+
+    snapshot = _FileJournal._snapshot
+    snapshotted = []
+
+    def snapshot_without_user_files(self, source, destination):
+        snapshotted.append(source)
+        assert source != reference and source != reference.parent
+        if source == skill_dir and user_reference:
+            assert not any(source.iterdir())
+        return snapshot(self, source, destination)
+
+    monkeypatch.setattr(_FileJournal, "_snapshot", snapshot_without_user_files)
+    args = ["preset", "remove", "my-preset"] if operation == "remove" else ["integration", "switch", "claude"]
+    previous_umask = os.umask(0o022)
+    try:
+        with pytest.raises(RuntimeError, match="failure after cleanup"):
+            with _transaction(project, "claude", _read_integration_json(project), read_records(project)):
+                result = runner.invoke(app, args, catch_exceptions=False)
+                assert result.exit_code == 0, result.output
+                assert not skill_file.exists()
+                assert skill_dir.exists() == user_reference
+                if user_reference:
+                    reference.write_bytes(b"User reference edited during transaction")
+                raise RuntimeError("failure after cleanup")
+    finally:
+        os.umask(previous_umask)
+
+    assert skill_file.read_bytes() == original
+    if os.name != "nt":
+        assert stat.S_IMODE(skill_dir.stat().st_mode) == 0o700
+    if user_reference:
+        assert skill_dir not in snapshotted
+        assert reference.read_bytes() == b"User reference edited during transaction"
+    assert "Recovery snapshots retained" not in capsys.readouterr().out