diff --git a/dataflow/utils/storage.py b/dataflow/utils/storage.py
index 09de9141..62659b83 100644
--- a/dataflow/utils/storage.py
+++ b/dataflow/utils/storage.py
@@ -391,7 +391,8 @@ def flush_step(self, step: int):
 
             os.replace(tmp_path, file_path)
             with self._lock:
-                self._dirty_steps.discard(step)
+                if self._buffers.get(step) is df:
+                    self._dirty_steps.discard(step)
             self.logger.success(f"[flush] Persisted step {step} -> {file_path}")
         finally:
             try:
diff --git a/test/cpu_only/test_lazy_file_storage_flush_concurrency.py b/test/cpu_only/test_lazy_file_storage_flush_concurrency.py
new file mode 100644
index 00000000..2e444fbb
--- /dev/null
+++ b/test/cpu_only/test_lazy_file_storage_flush_concurrency.py
@@ -0,0 +1,68 @@
+"""Concurrency regression tests for LazyFileStorage flush generation handling."""
+
+from pathlib import Path
+from threading import Event, Thread
+
+import pandas as pd
+import pytest
+
+from dataflow.utils import storage as storage_module
+from dataflow.utils.storage import LazyFileStorage
+
+pytestmark = pytest.mark.cpu
+
+
+def _make_storage(tmp_path):
+    source = tmp_path / "source.csv"
+    source.write_text("text\nsource\n", encoding="utf-8")
+    return LazyFileStorage(
+        str(source),
+        cache_path=str(tmp_path / "cache"),
+        cache_type="jsonl",
+        save_on_exit=False,
+    )
+
+
+def test_write_during_older_flush_remains_dirty_and_persistable(tmp_path, monkeypatch):
+    storage = _make_storage(tmp_path)
+    step = storage.step()
+    output = Path(step.write([{"text": "old generation"}]))
+
+    replace_entered = Event()
+    release_replace = Event()
+    original_replace = storage_module.os.replace
+
+    def blocking_replace(src, dst):
+        # Synchronize below LazyFileStorage.flush_step(): the real flush has
+        # already selected and serialized its old dataframe snapshot here.
+        replace_entered.set()
+        assert release_replace.wait(timeout=10), "test failed to release blocked persistence"
+        return original_replace(src, dst)
+
+    monkeypatch.setattr(storage_module.os, "replace", blocking_replace)
+
+    flush_thread = Thread(target=storage.flush_step, args=(1,))
+    flush_thread.start()
+    assert replace_entered.wait(timeout=10), "flush never reached persistence boundary"
+
+    # Real concurrent write to the same output step while the older flush is paused.
+    step.write([{"text": "new generation"}])
+
+    release_replace.set()
+    flush_thread.join(timeout=10)
+    assert not flush_thread.is_alive()
+
+    # The completed old flush may persist only its selected snapshot.
+    assert pd.read_json(output, lines=True).to_dict("records") == [
+        {"text": "old generation"}
+    ]
+
+    # Restore real persistence and use the normal public flush path. The newer
+    # write must still be considered dirty so flush_all() persists it.
+    monkeypatch.setattr(storage_module.os, "replace", original_replace)
+    storage.flush_all()
+
+    assert pd.read_json(output, lines=True).to_dict("records") == [
+        {"text": "new generation"}
+    ]
+    assert 1 not in storage._dirty_steps