diff --git a/scripts/prepare_trace_windows.py b/scripts/prepare_trace_windows.py
index edab4f5..89b18ad 100644
--- a/scripts/prepare_trace_windows.py
+++ b/scripts/prepare_trace_windows.py
@@ -3,6 +3,7 @@ from __future__ import annotations
 import argparse
 import hashlib
 import json
+import os
 from pathlib import Path
 from typing import Any
 from dataclasses import dataclass
@@ -222,10 +223,19 @@ def materialize_windows(
 
     stats_by_window = {str(window["window_id"]): WindowStats() for window in windows}
     handles: dict[str, Any] = {}
+    final_paths: dict[str, Path] = {}
+    temp_paths: dict[str, Path] = {}
+    completed = False
     try:
         for window in windows:
             window_id = str(window["window_id"])
-            handles[window_id] = (traces_dir / f"{window_id}.jsonl").open("w", encoding="utf-8")
+            final_path = traces_dir / f"{window_id}.jsonl"
+            temp_path = traces_dir / f".{window_id}.jsonl.tmp.{os.getpid()}"
+            if temp_path.exists():
+                temp_path.unlink()
+            final_paths[window_id] = final_path
+            temp_paths[window_id] = temp_path
+            handles[window_id] = temp_path.open("w", encoding="utf-8")
 
         for trace_path, prompt_path in sorted(grouped.keys()):
             bucket = grouped[(trace_path, prompt_path)]
@@ -270,9 +280,17 @@ def materialize_windows(
                 f"materialized {trace_path.name} -> matched_rows={matched_rows}",
                 flush=True,
             )
+        completed = True
     finally:
         for handle in handles.values():
             handle.close()
+        if completed:
+            for window_id, temp_path in temp_paths.items():
+                os.replace(temp_path, final_paths[window_id])
+        else:
+            for temp_path in temp_paths.values():
+                if temp_path.exists():
+                    temp_path.unlink()
     return stats_by_window
 
 
@@ -342,10 +360,17 @@ def main() -> int:
         "window_duration_seconds": 600.0,
         "windows": rendered_windows,
     }
-    (output_root / "windows.json").write_text(
-        json.dumps(windows_payload, ensure_ascii=False, indent=2) + "\n",
-        encoding="utf-8",
-    )
+    windows_path = output_root / "windows.json"
+    windows_tmp_path = output_root / f".windows.json.tmp.{os.getpid()}"
+    try:
+        windows_tmp_path.write_text(
+            json.dumps(windows_payload, ensure_ascii=False, indent=2) + "\n",
+            encoding="utf-8",
+        )
+        os.replace(windows_tmp_path, windows_path)
+    finally:
+        if windows_tmp_path.exists():
+            windows_tmp_path.unlink()
     print(output_root)
     print(f"windows={len(rendered_windows)}")
     return 0
diff --git a/tests/test_core_flow.py b/tests/test_core_flow.py
index bfbc6ea..7d2dff9 100644
--- a/tests/test_core_flow.py
+++ b/tests/test_core_flow.py
@@ -853,6 +853,64 @@ class CoreFlowTests(unittest.TestCase):
             self.assertEqual(rows[0]["output_length"], 7)
             self.assertIsInstance(rows[0]["sampling_u"], float)
 
+    def test_prepare_trace_windows_preserves_existing_files_on_failure(self) -> None:
+        with tempfile.TemporaryDirectory() as tmp:
+            tmp_path = Path(tmp)
+            legacy_source = tmp_path / "legacy"
+            thinking_source = tmp_path / "thinking"
+            output_root = tmp_path / "trace_windows"
+            traces_dir = output_root / "traces"
+            legacy_source.mkdir()
+            thinking_source.mkdir()
+            traces_dir.mkdir(parents=True)
+
+            for filename in [
+                "qwen_chat_blksz_64_031109-031111",
+                "qwen_chat_blksz_64_031121-031123",
+            ]:
+                for suffix in [".jsonl", "_prompt.jsonl"]:
+                    path = legacy_source / f"{filename}{suffix}"
+                    path.write_text(
+                        json.dumps(
+                            {
+                                "chat_id": "c1",
+                                "turn": 1,
+                                "timestamp": 3605.0,
+                                "input_length": 20,
+                                "output_length": 7,
+                                "prompt": "prompt",
+                            }
+                        )
+                        + "\n",
+                        encoding="utf-8",
+                    )
+
+            sentinel = traces_dir / "chat_w20260311_1000.jsonl"
+            sentinel.write_text("sentinel\n", encoding="utf-8")
+
+            proc = subprocess.run(
+                [
+                    "python3",
+                    "scripts/prepare_trace_windows.py",
+                    "--legacy-source",
+                    str(legacy_source),
+                    "--thinking-source",
+                    str(thinking_source),
+                    "--output-root",
+                    str(output_root),
+                    "--workloads",
+                    "chat",
+                    "--overwrite",
+                ],
+                cwd="/home/gahow/phd/aituner",
+                capture_output=True,
+                text=True,
+            )
+
+            self.assertNotEqual(proc.returncode, 0)
+            self.assertEqual(sentinel.read_text(encoding="utf-8"), "sentinel\n")
+            self.assertEqual(sorted(path.name for path in traces_dir.glob("*.tmp.*")), [])
+
     def test_binary_search_max_feasible(self) -> None:
         result = binary_search_max_feasible(
             low=0.0,