diff --git a/backend/packages/harness/deerflow/skills/mutations/publication.py b/backend/packages/harness/deerflow/skills/mutations/publication.py
index 8191d5fb5a..f291f27ab5 100644
--- a/backend/packages/harness/deerflow/skills/mutations/publication.py
+++ b/backend/packages/harness/deerflow/skills/mutations/publication.py
@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import logging
 import os
 import stat
 
@@ -12,6 +13,8 @@ from deerflow.skills.mutations.assets import capture_package, open_directory_cha
 from deerflow.skills.mutations.codec import operation_packages
 from deerflow.skills.mutations.repository import supersede_views
 
+logger = logging.getLogger(__name__)
+
 
 def replace_main(root, content: bytes, *, operation_id: str) -> None:
     """Use the validated directory descriptor throughout; preserve mode bits."""
@@ -48,6 +51,12 @@ def replace_main(root, content: bytes, *, operation_id: str) -> None:
                     os.unlink(temporary, dir_fd=parent)
                 except FileNotFoundError:
                     pass
+                except OSError:
+                    # The publication outcome is already decided; a leftover
+                    # temp is reported here and detected again by
+                    # ``assert_temporary_absent``, so it must not replace that
+                    # outcome with the cleanup error.
+                    logger.warning("Failed to remove skill mutation temporary %s", temporary, exc_info=True)
         finally:
             os.close(directory)
             if parent is not None:
diff --git a/backend/tests/test_skill_publication_cleanup.py b/backend/tests/test_skill_publication_cleanup.py
new file mode 100644
index 0000000000..b5dbe7bf7b
--- /dev/null
+++ b/backend/tests/test_skill_publication_cleanup.py
@@ -0,0 +1,60 @@
+"""A failed discard must not replace the outcome of a skill publication.
+
+``replace_main`` publishes ``SKILL.md`` through a ``.host-mutation-*`` sibling and
+discards it on exit. That discard only tolerated ``FileNotFoundError``, so any
+other ``OSError`` replaced the publish error — or turned a decided outcome into a
+cleanup failure. A leftover temp is still caught later by
+``assert_temporary_absent``, so reporting is enough here.
+"""
+
+from __future__ import annotations
+
+import os
+
+import pytest
+
+# ``replace_main`` walks directory descriptors with ``O_DIRECTORY``/``O_NOFOLLOW``.
+pytestmark = pytest.mark.skipif(os.name != "posix", reason="host skill mutation tests require POSIX filesystem primitives")
+
+
+def _make_skill_dir(tmp_path):
+    root = tmp_path / "skills" / "example"
+    root.mkdir(parents=True)
+    (root / "SKILL.md").write_text("original\n", encoding="utf-8")
+    return root
+
+
+def test_replace_main_keeps_the_publish_error_when_cleanup_fails(tmp_path, monkeypatch, caplog):
+    from deerflow.skills.mutations import publication
+
+    root = _make_skill_dir(tmp_path)
+    real_unlink = publication.os.unlink
+
+    def failing_fsync(_fd):
+        raise OSError("disk error")
+
+    def failing_unlink(path, *args, **kwargs):
+        if str(path).startswith(".host-mutation-"):
+            raise PermissionError("temporary is still open")
+        return real_unlink(path, *args, **kwargs)
+
+    monkeypatch.setattr(publication.os, "fsync", failing_fsync)
+    monkeypatch.setattr(publication.os, "unlink", failing_unlink)
+
+    with caplog.at_level("WARNING", logger="deerflow.skills.mutations.publication"):
+        with pytest.raises(OSError, match="disk error"):
+            publication.replace_main(root, b"replacement\n", operation_id="cleanup")
+
+    assert (root / "SKILL.md").read_text(encoding="utf-8") == "original\n"
+    assert "Failed to remove skill mutation temporary" in caplog.text
+
+
+def test_replace_main_still_publishes_and_removes_the_temporary(tmp_path):
+    from deerflow.skills.mutations import publication
+
+    root = _make_skill_dir(tmp_path)
+
+    publication.replace_main(root, b"replacement\n", operation_id="clean")
+
+    assert (root / "SKILL.md").read_text(encoding="utf-8") == "replacement\n"
+    assert [p.name for p in root.parent.iterdir() if p.name.startswith(".host-mutation-")] == []