diff --git a/frontend/src/pages/DataAnnotation/Annotate/LabelStudioTextEditor.tsx b/frontend/src/pages/DataAnnotation/Annotate/LabelStudioTextEditor.tsx
index 5f3192c..9fdc324 100644
--- a/frontend/src/pages/DataAnnotation/Annotate/LabelStudioTextEditor.tsx
+++ b/frontend/src/pages/DataAnnotation/Annotate/LabelStudioTextEditor.tsx
@@ -9,7 +9,7 @@ import {
   listEditorTasksUsingGet,
   upsertEditorAnnotationUsingPut,
   checkFileVersionUsingGet,
-  useNewVersionUsingPost,
+  applyNewVersionUsingPost,
   type FileVersionCheckResponse,
 } from "../annotation.api";
 import { AnnotationResultStatus } from "../annotation.model";
@@ -232,6 +232,7 @@ export default function LabelStudioTextEditor() {
   const origin = useMemo(() => window.location.origin, []);
   const iframeRef = useRef<HTMLIFrameElement | null>(null);
   const initSeqRef = useRef(0);
+  const fileVersionCheckSeqRef = useRef(0);
   const expectedTaskIdRef = useRef<number | null>(null);
   const prefetchSeqRef = useRef(0);
   const exportCheckRef = useRef<{
@@ -274,7 +275,7 @@ export default function LabelStudioTextEditor() {
 
   // 文件版本相关状态
   const [fileVersionInfo, setFileVersionInfo] = useState<FileVersionCheckResponse | null>(null);
-  const [checkingFileVersion, setCheckingFileVersion] = useState(false);
+  const [, setCheckingFileVersion] = useState(false);
   const [usingNewVersion, setUsingNewVersion] = useState(false);
 
   const focusIframe = useCallback(() => {
@@ -558,9 +559,11 @@ export default function LabelStudioTextEditor() {
 
   const checkFileVersion = useCallback(async (fileId: string) => {
     if (!projectId || !fileId) return;
+    const seq = ++fileVersionCheckSeqRef.current;
     setCheckingFileVersion(true);
     try {
       const resp = (await checkFileVersionUsingGet(projectId, fileId)) as ApiResponse<FileVersionCheckResponse>;
+      if (seq !== fileVersionCheckSeqRef.current) return;
       const data = resp?.data;
       if (data) {
         setFileVersionInfo(data);
@@ -584,9 +587,9 @@ export default function LabelStudioTextEditor() {
     } catch (e) {
       console.error("检查文件版本失败", e);
     } finally {
-      setCheckingFileVersion(false);
+      if (seq === fileVersionCheckSeqRef.current) setCheckingFileVersion(false);
     }
-  }, [modal, message, projectId]);
+  }, [modal, projectId]);
 
   const handleUseNewVersion = useCallback(async () => {
     if (!selectedFileId) return;
@@ -612,7 +615,7 @@ export default function LabelStudioTextEditor() {
         if (!projectId || !selectedFileId) return;
         setUsingNewVersion(true);
         try {
-          await useNewVersionUsingPost(projectId, selectedFileId);
+          await applyNewVersionUsingPost(projectId, selectedFileId);
           message.success("已使用新版本并清空标注");
           setFileVersionInfo(null);
           await loadTasks({ mode: "reset" });
@@ -985,7 +988,7 @@ export default function LabelStudioTextEditor() {
           {fileVersionInfo?.hasNewVersion && (
             <div className="flex items-center gap-2 mr-4">
               <Typography.Text type="warning" className="text-xs">
-                ⚠ 文件有新版本（{fileVersionInfo.currentFileVersion} > {fileVersionInfo.annotationFileVersion}）
+                ⚠ 文件有新版本（{fileVersionInfo.currentFileVersion}{" > "}{fileVersionInfo.annotationFileVersion}）
               </Typography.Text>
               <Button
                 size="small"
@@ -998,6 +1001,11 @@ export default function LabelStudioTextEditor() {
               </Button>
             </div>
           )}
+          {fileVersionInfo?.annotationVersionUnknown && !fileVersionInfo?.hasNewVersion && (
+            <Typography.Text type="secondary" className="text-xs mr-4">
+              历史标注缺少文件版本信息，保存后将绑定当前版本（{fileVersionInfo.currentFileVersion}）
+            </Typography.Text>
+          )}
           <Button
             type="primary"
             icon={<SaveOutlined />}
diff --git a/frontend/src/pages/DataAnnotation/annotation.api.ts b/frontend/src/pages/DataAnnotation/annotation.api.ts
index 39d3b20..7cb54fa 100644
--- a/frontend/src/pages/DataAnnotation/annotation.api.ts
+++ b/frontend/src/pages/DataAnnotation/annotation.api.ts
@@ -104,6 +104,7 @@ export interface FileVersionCheckResponse {
   fileId: string;
   currentFileVersion: number;
   annotationFileVersion: number | null;
+  annotationVersionUnknown: boolean;
   hasNewVersion: boolean;
 }
 
@@ -118,7 +119,7 @@ export interface UseNewVersionResponse {
   message: string;
 }
 
-export function useNewVersionUsingPost(projectId: string, fileId: string) {
+export function applyNewVersionUsingPost(projectId: string, fileId: string) {
   return post(`/api/annotation/editor/projects/${projectId}/files/${fileId}/use-new-version`, {});
 }
 
diff --git a/runtime/datamate-python/alembic/env.py b/runtime/datamate-python/alembic/env.py
index c56aeb4..748db97 100644
--- a/runtime/datamate-python/alembic/env.py
+++ b/runtime/datamate-python/alembic/env.py
@@ -1,27 +1,47 @@
-"""Alembic environment configuration"""
+"""Alembic environment configuration
 
-from logging.config import fileConfig
-from sqlalchemy import engine_from_config, pool
-from alembic import context
-import sys
+说明：
+- DataMate Python 服务使用异步 SQLAlchemy（mysql+aiomysql）。
+- 为了让 `alembic upgrade head` 开箱即用，这里自动从 `settings.database_url`
+  注入 `sqlalchemy.url`，无需在 alembic.ini 手工维护。
+"""
+
+from __future__ import annotations
+
+import asyncio
 import os
+import sys
+from logging.config import fileConfig
 
-# 添加项目路径
+from alembic import context
+from sqlalchemy import pool
+from sqlalchemy.ext.asyncio import async_engine_from_config
+
+# 添加项目路径（runtime/datamate-python）
 sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
 
+from app.core.config import settings
 from app.db.session import Base
-from app.db.models import *
+from app.db.models import *  # noqa: F401,F403
 
 config = context.config
+
 if config.config_file_name is not None:
     fileConfig(config.config_file_name)
 
+# 自动注入 sqlalchemy.url（优先使用 settings.database_url）
+if not config.get_main_option("sqlalchemy.url"):
+    config.set_main_option("sqlalchemy.url", settings.database_url)
+
 target_metadata = Base.metadata
 
 
 def run_migrations_offline() -> None:
     """Run migrations in 'offline' mode."""
     url = config.get_main_option("sqlalchemy.url")
+    if not url:
+        raise RuntimeError("alembic 未配置 sqlalchemy.url，且无法从 settings.database_url 推导")
+
     context.configure(
         url=url,
         target_metadata=target_metadata,
@@ -33,19 +53,29 @@ def run_migrations_offline() -> None:
         context.run_migrations()
 
 
-def run_migrations_online() -> None:
-    """Run migrations in 'online' mode."""
-    connectable = engine_from_config(
+def do_run_migrations(connection) -> None:
+    context.configure(connection=connection, target_metadata=target_metadata)
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_async_migrations() -> None:
+    connectable = async_engine_from_config(
         config.get_section(config.config_ini_section, {}),
         prefix="sqlalchemy.",
         poolclass=pool.NullPool,
     )
 
-    with connectable.connect() as connection:
-        context.configure(connection=connection, target_metadata=target_metadata)
+    async with connectable.connect() as connection:
+        await connection.run_sync(do_run_migrations)
 
-        with context.begin_transaction():
-            context.run_migrations()
+    await connectable.dispose()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode."""
+    asyncio.run(run_async_migrations())
 
 
 if context.is_offline_mode():
diff --git a/runtime/datamate-python/app/module/annotation/schema/editor.py b/runtime/datamate-python/app/module/annotation/schema/editor.py
index b512ff1..0111e62 100644
--- a/runtime/datamate-python/app/module/annotation/schema/editor.py
+++ b/runtime/datamate-python/app/module/annotation/schema/editor.py
@@ -205,6 +205,11 @@ class FileVersionCheckResponse(BaseModel):
     annotation_file_version: Optional[int] = Field(
         None, alias="annotationFileVersion", description="标注时的文件版本"
     )
+    annotation_version_unknown: bool = Field(
+        False,
+        alias="annotationVersionUnknown",
+        description="是否缺少标注时的文件版本（历史数据）",
+    )
     has_new_version: bool = Field(
         ..., alias="hasNewVersion", description="是否有新版本"
     )
diff --git a/runtime/datamate-python/app/module/annotation/service/editor.py b/runtime/datamate-python/app/module/annotation/service/editor.py
index c5777e2..8cdca0b 100644
--- a/runtime/datamate-python/app/module/annotation/service/editor.py
+++ b/runtime/datamate-python/app/module/annotation/service/editor.py
@@ -1500,6 +1500,7 @@ class AnnotationEditorService:
         for file_record in valid_files:
             file_id = str(file_record.id)  # type: ignore
             file_name = str(getattr(file_record, "file_name", ""))
+            current_file_version = getattr(file_record, "version", None)
 
             for retry in range(max_retries):
                 try:
@@ -1602,6 +1603,7 @@ class AnnotationEditorService:
                         # 更新现有标注
                         existing.annotation = final_payload  # type: ignore[assignment]
                         existing.annotation_status = ANNOTATION_STATUS_IN_PROGRESS  # type: ignore[assignment]
+                        existing.file_version = current_file_version  # type: ignore[assignment]
                         existing.updated_at = now  # type: ignore[assignment]
                     else:
                         # 创建新标注记录
@@ -1611,6 +1613,7 @@ class AnnotationEditorService:
                             file_id=file_id,
                             annotation=final_payload,
                             annotation_status=ANNOTATION_STATUS_IN_PROGRESS,
+                            file_version=current_file_version,
                             created_at=now,
                             updated_at=now,
                         )
@@ -1679,18 +1682,21 @@ class AnnotationEditorService:
         current_file_version = file_record.version
         annotation_file_version = annotation.file_version if annotation else None
 
-        if annotation is None:
-            has_new_version = False
-        elif annotation_file_version is None:
-            has_new_version = True
-        else:
-            has_new_version = current_file_version > annotation_file_version
+        annotation_version_unknown = (
+            annotation is not None and annotation_file_version is None
+        )
+        has_new_version = (
+            current_file_version > annotation_file_version
+            if annotation_file_version is not None
+            else False
+        )
 
         return {
             "fileId": file_id,
             "currentFileVersion": current_file_version,
             "annotationFileVersion": annotation_file_version,
             "hasNewVersion": has_new_version,
+            "annotationVersionUnknown": annotation_version_unknown,
         }
 
     async def use_new_version(self, project_id: str, file_id: str) -> Dict[str, Any]:
@@ -1749,24 +1755,31 @@ class AnnotationEditorService:
 
         # 清空标注并更新版本号
         now = datetime.utcnow()
-        if isinstance(annotation.annotation, dict):
-            if annotation.annotation.get(SEGMENTED_KEY):
-                segments = annotation.annotation.get(SEGMENTS_KEY, {})
-                for segment_id, segment_data in segments.items():
-                    if isinstance(segment_data, dict):
-                        segment_data[SEGMENT_RESULT_KEY] = []
-                annotation.annotation = {
-                    SEGMENTED_KEY: True,
-                    "version": annotation.annotation.get("version", 1),
-                    SEGMENTS_KEY: segments,
-                    "total_segments": annotation.annotation.get(
-                        "total_segments", len(segments)
-                    ),
-                }
-            else:
-                annotation.annotation = {}
-        else:
-            annotation.annotation = {}
+        cleared_payload: Dict[str, Any] = {}
+        if isinstance(annotation.annotation, dict) and self._is_segmented_annotation(
+            annotation.annotation
+        ):
+            segments = self._extract_segment_annotations(annotation.annotation)
+            cleared_segments: Dict[str, Dict[str, Any]] = {}
+            for segment_id, segment_data in segments.items():
+                if not isinstance(segment_data, dict):
+                    continue
+                normalized = dict(segment_data)
+                normalized[SEGMENT_RESULT_KEY] = []
+                cleared_segments[str(segment_id)] = normalized
+
+            total_segments = self._resolve_segment_total(annotation.annotation)
+            if total_segments is None:
+                total_segments = len(cleared_segments)
+
+            cleared_payload = {
+                SEGMENTED_KEY: True,
+                "version": annotation.annotation.get("version", 1),
+                SEGMENTS_KEY: cleared_segments,
+                SEGMENT_TOTAL_KEY: total_segments,
+            }
+
+        annotation.annotation = cleared_payload
         annotation.annotation_status = ANNOTATION_STATUS_NO_ANNOTATION
         annotation.file_version = current_file_version
         annotation.updated_at = now
@@ -1774,6 +1787,13 @@ class AnnotationEditorService:
         await self.db.commit()
         await self.db.refresh(annotation)
 
+        await self._sync_annotation_to_knowledge(
+            project,
+            file_record,
+            cleared_payload,
+            annotation.updated_at or now,
+        )
+
         return {
             "fileId": file_id,
             "previousFileVersion": previous_file_version,