diff --git a/app/harness/store.py b/app/harness/store.py
index 49509d9..87fba07 100644
--- a/app/harness/store.py
+++ b/app/harness/store.py
@@ -266,7 +266,9 @@ def read_seed(store_dir: Path, name: str) -> dict:
     return json.loads(seed_json.read_text())
 
 
-def extract_run_db(src_db: Path, dst_db: Path, run_id: str) -> None:
+def extract_run_db(
+    src_db: Path, dst_db: Path, run_id: str, *, dedupe_per_question: bool = False
+) -> None:
     """从 src_db 抽出某 run_id 的 _runs + predictions 行，写一个最小 db（种子 baseline.db）。
 
     用源表的**原始 CREATE 语句**重建目标表，保留主键/列类型/约束——
@@ -277,6 +279,9 @@ def extract_run_db(src_db: Path, dst_db: Path, run_id: str) -> None:
         src_db: 源 harness.db。
         dst_db: 目标 db（不得已存在）。
         run_id: 要抽取的 run。
+        dedupe_per_question: True 时 predictions 表每 question_id 仅保留 rowid 最小
+            的首行（对齐 canonical「每 question_id 取第一行 ORDER BY rowid」口径，
+            902→900）。_runs 表不受影响。
 
     异常:
         RuntimeError: 源中无该表或无该 run 的行。
@@ -294,9 +299,17 @@ def extract_run_db(src_db: Path, dst_db: Path, run_id: str) -> None:
             dst.execute(create_sql[0])
             cols = [r[1] for r in src.execute(f"PRAGMA table_info({table})")]
             col_sql = ", ".join(cols)
-            rows = src.execute(
-                f"SELECT {col_sql} FROM {table} WHERE run_id=?", (run_id,)
-            ).fetchall()
+            if table == "predictions" and dedupe_per_question:
+                rows = src.execute(
+                    f"SELECT {col_sql} FROM {table} WHERE run_id=? "
+                    "AND rowid IN (SELECT MIN(rowid) FROM predictions "
+                    "WHERE run_id=? GROUP BY question_id)",
+                    (run_id, run_id),
+                ).fetchall()
+            else:
+                rows = src.execute(
+                    f"SELECT {col_sql} FROM {table} WHERE run_id=?", (run_id,)
+                ).fetchall()
             if not rows:
                 raise RuntimeError(f"{table} 中无 run_id={run_id} 的行")
             ph = ", ".join("?" * len(cols))
diff --git a/tests/unit/test_harness_store.py b/tests/unit/test_harness_store.py
index 63bbaf0..721366b 100644
--- a/tests/unit/test_harness_store.py
+++ b/tests/unit/test_harness_store.py
@@ -338,6 +338,44 @@ class TestExtractRunDb:
         with pytest.raises(RuntimeError, match="无 run_id="):
             extract_run_db(src, dst, "nonexistent")
 
+    def test_dedupe_per_question_keeps_first_row(self, tmp_path):
+        """dedupe_per_question=True 时每 question_id 只保留 rowid 最小的首行。"""
+        import sqlite3
+
+        src = tmp_path / "src.db"
+        conn = sqlite3.connect(src)
+        conn.execute(
+            "CREATE TABLE _runs (run_id TEXT PRIMARY KEY, started_at TEXT)"
+        )
+        conn.execute("INSERT INTO _runs VALUES ('r1', 't0')")
+        conn.execute(
+            "CREATE TABLE predictions (run_id TEXT, question_id TEXT, prediction TEXT)"
+        )
+        # 743-1 三行（模拟 error/budget/finished），首行 prediction=NULL
+        conn.executemany(
+            "INSERT INTO predictions VALUES (?,?,?)",
+            [
+                ("r1", "743-1", None),
+                ("r1", "743-1", None),
+                ("r1", "743-1", "C"),
+                ("r1", "q2", "A"),
+            ],
+        )
+        conn.commit()
+        conn.close()
+
+        dst = tmp_path / "dst.db"
+        from app.harness.store import extract_run_db
+
+        extract_run_db(src, dst, "r1", dedupe_per_question=True)
+
+        out = sqlite3.connect(dst)
+        rows = out.execute(
+            "SELECT question_id, prediction FROM predictions ORDER BY question_id"
+        ).fetchall()
+        out.close()
+        assert rows == [("743-1", None), ("q2", "A")], f"未按 rowid 首行去重: {rows}"
+
 
 # ---------------------------------------------------------------------------
 # promote_to_seed