diff --git a/CHANGELOG.md b/CHANGELOG.md
index ba10337a..74ebde3f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@
 ### Fixed
 
 - `rebuild --embed-only` re-embeds picture chunks through the image path instead of overwriting their vectors with a text embedding of the caption.
+- DELETE jobs re-check the source with `head()` before deleting and skip when the resource is back, so an atomic-rename save (vim, `git checkout`) no longer blackholes a live document.
 
 ## [0.52.0] - 2026-06-01
 
diff --git a/haiku_rag_slim/haiku/rag/ingester/workers/pipeline.py b/haiku_rag_slim/haiku/rag/ingester/workers/pipeline.py
index 105bc417..b59e105c 100644
--- a/haiku_rag_slim/haiku/rag/ingester/workers/pipeline.py
+++ b/haiku_rag_slim/haiku/rag/ingester/workers/pipeline.py
@@ -9,6 +9,7 @@ from haiku.rag.client.exceptions import UnsupportedSourceError
 from haiku.rag.ingester.exceptions import PermanentError, TransientError
 from haiku.rag.ingester.queue.models import Job, JobOp
 from haiku.rag.ingester.sources.base import FileTooLargeError
+from haiku.rag.ingester.sources.registry import resolve_configured_source
 from haiku.rag.telemetry import attach_context, logfire
 
 if TYPE_CHECKING:
@@ -105,6 +106,17 @@ async def run_job(
     ):
         try:
             if job.op is JobOp.DELETE:
+                # An atomic-rename save can let a spurious DELETE win the
+                # enqueue race while the file is mid-rewrite. If the resource
+                # is already back, skip the delete (it would blackhole a live
+                # document) and let the next sweep re-ingest it.
+                try:
+                    source = resolve_configured_source(job.uri, job.source_id, sources)
+                    restored = await source.head(job.uri) is not None
+                except Exception:
+                    restored = False
+                if restored:
+                    return JobResult(deleted=False)
                 doc = await client.get_document_by_uri(job.uri)
                 if doc is not None and doc.id is not None:
                     await client.delete_document(doc.id)
diff --git a/tests/ingester/test_pipeline.py b/tests/ingester/test_pipeline.py
index 59110d71..62d2cedf 100644
--- a/tests/ingester/test_pipeline.py
+++ b/tests/ingester/test_pipeline.py
@@ -7,7 +7,7 @@ import pytest
 from haiku.rag.client import HaikuRAG
 from haiku.rag.ingester.exceptions import PermanentError, TransientError
 from haiku.rag.ingester.queue.models import Job, JobOp, JobStatus
-from haiku.rag.ingester.sources.base import FileTooLargeError
+from haiku.rag.ingester.sources.base import FetchResult, FileTooLargeError, Source
 from haiku.rag.ingester.workers.pipeline import run_job
 from haiku.rag.store.models.document import Document
 
@@ -104,6 +104,91 @@ async def test_delete_is_noop_when_document_missing():
     client.delete_document.assert_not_awaited()
 
 
+class _StubSource:
+    """Source double whose head() returns a scripted revision or raises."""
+
+    def __init__(
+        self,
+        source_id: str,
+        revision: str | None,
+        *,
+        head_error: Exception | None = None,
+    ):
+        self.source_id = source_id
+        self._revision = revision
+        self._head_error = head_error
+
+    def supports(self, uri: str) -> bool:
+        return True
+
+    async def head(self, uri: str) -> str | None:
+        if self._head_error is not None:
+            raise self._head_error
+        return self._revision
+
+    async def aclose(self) -> None: ...
+
+    async def fetch(self, uri: str) -> FetchResult:  # pragma: no cover - unused
+        raise NotImplementedError
+
+    async def discover(self, since=None, *, known_uris=None):  # pragma: no cover
+        raise NotImplementedError
+        yield
+
+
+@pytest.mark.asyncio
+async def test_delete_skipped_when_resource_restored_on_source():
+    """The file is back on disk by the time the DELETE runs, so head()
+    returns a revision and the delete is skipped — otherwise a live document
+    gets blackholed until the next sweep."""
+    client = _mock_client()
+    client.get_document_by_uri.return_value = Document(id="doc-9", content="", uri="u")
+    sources: list[Source] = [_StubSource("src", "12345")]
+
+    result = await run_job(client, _job(op=JobOp.DELETE), sources=sources)
+
+    assert result.deleted is False
+    client.delete_document.assert_not_awaited()
+
+
+@pytest.mark.asyncio
+async def test_delete_proceeds_when_resource_absent_on_source():
+    client = _mock_client()
+    client.get_document_by_uri.return_value = Document(id="doc-9", content="", uri="u")
+    sources: list[Source] = [_StubSource("src", None)]
+
+    result = await run_job(client, _job(op=JobOp.DELETE), sources=sources)
+
+    assert result.deleted is True
+    client.delete_document.assert_awaited_once_with("doc-9")
+
+
+@pytest.mark.asyncio
+async def test_delete_proceeds_when_source_unresolvable():
+    """No configured source for the job: the probe can't run, so the delete
+    proceeds exactly as before."""
+    client = _mock_client()
+    client.get_document_by_uri.return_value = Document(id="doc-9", content="", uri="u")
+
+    result = await run_job(client, _job(op=JobOp.DELETE), sources=[])
+
+    assert result.deleted is True
+    client.delete_document.assert_awaited_once_with("doc-9")
+
+
+@pytest.mark.asyncio
+async def test_delete_proceeds_when_head_probe_raises():
+    """A failing head() probe must not block the delete."""
+    client = _mock_client()
+    client.get_document_by_uri.return_value = Document(id="doc-9", content="", uri="u")
+    sources: list[Source] = [_StubSource("src", None, head_error=OSError("boom"))]
+
+    result = await run_job(client, _job(op=JobOp.DELETE), sources=sources)
+
+    assert result.deleted is True
+    client.delete_document.assert_awaited_once_with("doc-9")
+
+
 @pytest.mark.asyncio
 async def test_unsupported_extension_classified_permanent():
     from haiku.rag.client.exceptions import UnsupportedSourceError