diff --git a/python/lean_pool/merge_queue_cleanup.py b/python/lean_pool/merge_queue_cleanup.py
index aba26a319c..d8bcd03483 100644
--- a/python/lean_pool/merge_queue_cleanup.py
+++ b/python/lean_pool/merge_queue_cleanup.py
@@ -36,12 +36,16 @@ def discarded_runs(
 
 def branch_exists(repository: str, branch: str) -> bool:
     """Report a branch as missing only on a definite 404, never on other errors."""
-    result = subprocess.run(
-        ["gh", "api", f"repos/{repository}/git/ref/heads/{branch}"],
-        capture_output=True,
-        text=True,
-        timeout=60,
-    )
+    try:
+        result = subprocess.run(
+            ["gh", "api", f"repos/{repository}/git/ref/heads/{branch}"],
+            capture_output=True,
+            text=True,
+            timeout=60,
+        )
+    except subprocess.TimeoutExpired:
+        LOGGER.warning("Timed out looking up %s; keeping its run", branch)
+        return True
     if result.returncode == 0:
         return True
     if "HTTP 404" in result.stderr:
@@ -75,20 +79,37 @@ def queue_runs(repository: str) -> list[dict[str, Any]]:
 
 
 def cancel_discarded(repository: str, current_run_id: int) -> list[int]:
-    """Cancel every discarded queue run and return the cancelled run IDs."""
-    cancelled = discarded_runs(
+    """Request cancellation of discarded runs and return accepted request IDs."""
+    discarded = discarded_runs(
         queue_runs(repository),
         current_run_id,
         lambda branch: branch_exists(repository, branch),
     )
-    for run_id in cancelled:
-        LOGGER.info("Cancelling run %s: its merge group was discarded", run_id)
-        subprocess.run(
-            ["gh", "run", "cancel", str(run_id), "--repo", repository],
-            check=False,
-            timeout=60,
+    accepted: list[int] = []
+    for run_id in discarded:
+        try:
+            result = subprocess.run(
+                ["gh", "run", "cancel", str(run_id), "--repo", repository],
+                check=False,
+                capture_output=True,
+                text=True,
+                timeout=60,
+            )
+        except subprocess.TimeoutExpired:
+            LOGGER.warning("Timed out requesting cancellation of run %s", run_id)
+            continue
+        if result.returncode != 0:
+            LOGGER.warning(
+                "Could not request cancellation of run %s: %s",
+                run_id,
+                result.stderr.strip(),
+            )
+            continue
+        LOGGER.info(
+            "Requested cancellation of run %s: its merge group was discarded", run_id
         )
-    return cancelled
+        accepted.append(run_id)
+    return accepted
 
 
 def main() -> None:
diff --git a/python/tests/test_merge_queue_cleanup.py b/python/tests/test_merge_queue_cleanup.py
index 67e9709e64..b4c91d4a30 100644
--- a/python/tests/test_merge_queue_cleanup.py
+++ b/python/tests/test_merge_queue_cleanup.py
@@ -82,3 +82,63 @@ def fake_run(command: list[str], **kwargs: Any) -> subprocess.CompletedProcess[s
     monkeypatch.setattr(subprocess, "run", fake_run)
     assert cancel_discarded("owner/repository", 99) == [1, 3]
     assert [command[3] for command in cancelled] == ["1", "3"]
+
+
+def test_ref_timeout_keeps_run_and_scans_later_discarded(
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """An unknown first ref must not hide a later definite missing ref."""
+    looked_up: list[str] = []
+    cancellation_requests: list[str] = []
+    monkeypatch.setattr(
+        merge_queue_cleanup,
+        "queue_runs",
+        lambda repository: [_run(1, GONE), _run(3, ALSO_GONE)],
+    )
+
+    def fake_run(command: list[str], **kwargs: Any) -> subprocess.CompletedProcess[str]:
+        if command[:2] == ["gh", "api"]:
+            looked_up.append(command[2])
+            if command[2] == f"repos/owner/repository/git/ref/heads/{GONE}":
+                raise subprocess.TimeoutExpired(command, 60)
+            assert command[2] == f"repos/owner/repository/git/ref/heads/{ALSO_GONE}"
+            return subprocess.CompletedProcess(command, 1, "", "HTTP 404")
+        assert command[:3] == ["gh", "run", "cancel"]
+        cancellation_requests.append(command[3])
+        return subprocess.CompletedProcess(command, 0, "", "")
+
+    monkeypatch.setattr(subprocess, "run", fake_run)
+    assert cancel_discarded("owner/repository", 99) == [3]
+    assert looked_up == [
+        f"repos/owner/repository/git/ref/heads/{GONE}",
+        f"repos/owner/repository/git/ref/heads/{ALSO_GONE}",
+    ]
+    assert cancellation_requests == ["3"]
+
+
+@pytest.mark.parametrize("failure", ["timeout", "nonzero"])
+def test_failed_cancellation_continues_and_returns_only_accepted(
+    monkeypatch: pytest.MonkeyPatch, failure: str
+) -> None:
+    """One failed request must not stop later requests or count as accepted."""
+    cancellation_requests: list[str] = []
+    monkeypatch.setattr(
+        merge_queue_cleanup,
+        "queue_runs",
+        lambda repository: [_run(1, GONE), _run(3, ALSO_GONE)],
+    )
+
+    def fake_run(command: list[str], **kwargs: Any) -> subprocess.CompletedProcess[str]:
+        if command[:2] == ["gh", "api"]:
+            return subprocess.CompletedProcess(command, 1, "", "HTTP 404")
+        assert command[:3] == ["gh", "run", "cancel"]
+        cancellation_requests.append(command[3])
+        if command[3] == "1":
+            if failure == "timeout":
+                raise subprocess.TimeoutExpired(command, 60)
+            return subprocess.CompletedProcess(command, 1, "", "HTTP 403")
+        return subprocess.CompletedProcess(command, 0, "", "")
+
+    monkeypatch.setattr(subprocess, "run", fake_run)
+    assert cancel_discarded("owner/repository", 99) == [3]
+    assert cancellation_requests == ["1", "3"]