diff --git a/src/borg/legacyrepository.py b/src/borg/legacyrepository.py
index 9cdd5f9811..5e626316e9 100644
--- a/src/borg/legacyrepository.py
+++ b/src/borg/legacyrepository.py
@@ -736,7 +736,12 @@ def complete_xfer(intermediate=True):
             for segment in unused:
                 logger.debug("complete_xfer: Deleting unused segment %d", segment)
                 count = self.segments.pop(segment)
-                assert count == 0, "Corrupted segment reference count - corrupted index or hints"
+                if count != 0:
+                    logger.warning(
+                        "Corrupted segment reference count %d (expected 0) for segment %d - corrupted index or hints",
+                        count,
+                        segment,
+                    )
                 self.io.delete_segment(segment)
                 del self.compact[segment]
             unused = []
@@ -748,7 +753,8 @@ def complete_xfer(intermediate=True):
         for segment, freeable_space in sorted(self.compact.items()):
             if not self.io.segment_exists(segment):
                 logger.warning("Segment %d not found, but listed in compaction data", segment)
-                del self.compact[segment]
+                self.compact.pop(segment, None)
+                self.segments.pop(segment, None)
                 pi.show()
                 self._send_log()
                 continue
@@ -867,7 +873,12 @@ def complete_xfer(intermediate=True):
                         if not self.shadow_index[key]:
                             # shadowed segments list is empty -> remove it
                             del self.shadow_index[key]
-            assert segments[segment] == 0, "Corrupted segment reference count - corrupted index or hints"
+            if segments[segment] != 0:
+                logger.warning(
+                    "Corrupted segment reference count %d (expected 0) for segment %d - corrupted index or hints",
+                    segments[segment],
+                    segment,
+                )
             unused.append(segment)
             pi.show()
             self._send_log()
diff --git a/src/borg/testsuite/legacyrepository_test.py b/src/borg/testsuite/legacyrepository_test.py
index 0b6a10aa5b..31bb5936f1 100644
--- a/src/borg/testsuite/legacyrepository_test.py
+++ b/src/borg/testsuite/legacyrepository_test.py
@@ -654,17 +654,20 @@ def test_subtly_corrupted_hints(repository):
         assert pdchunk(repository.get(H(2))) == b"bazz"
 
 
-def test_subtly_corrupted_hints_without_integrity(repository):
+def test_subtly_corrupted_hints_without_integrity(repository, caplog):
     make_auxiliary(repository)
     _subtly_corrupted_hints_setup(repository)
     integrity_path = os.path.join(repository.path, "integrity.5")
     os.unlink(integrity_path)
     with repository:
         repository.put(H(3), fchunk(b"1234"))
-        # do a compaction run, which fails since the corrupted refcount wasn't detected and causes an assertion failure.
-        with pytest.raises(AssertionError) as exc_info:
-            repository.commit(compact=True)
-        assert "Corrupted segment reference count" in str(exc_info.value)
+        # Do a compaction run.
+        # The corrupted refcount is detected and logged as a warning, but compaction proceeds.
+        caplog.set_level(logging.WARNING, logger="borg.legacyrepository")
+        repository.commit(compact=True)
+        assert "Corrupted segment reference count" in caplog.text
+        # We verify that the repository is still consistent.
+        assert repository.check()
 
 
 def list_indices(repo_path):