diff --git a/backend/package/yuxi/knowledge/base.py b/backend/package/yuxi/knowledge/base.py
index 278c8e8c..f2d74519 100644
--- a/backend/package/yuxi/knowledge/base.py
+++ b/backend/package/yuxi/knowledge/base.py
@@ -351,6 +351,18 @@ class KnowledgeBase(ABC):
 
         await self._persist_file(file_id)
 
+    async def _mark_file_unparsed(self, file_id: str, operator_id: str | None = None) -> None:
+        if file_id not in self.files_meta:
+            return
+
+        self.files_meta[file_id]["status"] = FileStatus.UPLOADED
+        self.files_meta[file_id].pop("markdown_file", None)
+        self.files_meta[file_id].pop("error", None)
+        self.files_meta[file_id]["updated_at"] = utc_isoformat()
+        if operator_id:
+            self.files_meta[file_id]["updated_by"] = operator_id
+        await self._persist_file(file_id)
+
     async def _save_markdown_to_minio(self, db_id: str, file_id: str, content: str) -> str:
         """Save markdown content to MinIO and return HTTP URL"""
         from yuxi.storage.minio import get_minio_client
diff --git a/backend/package/yuxi/knowledge/implementations/lightrag.py b/backend/package/yuxi/knowledge/implementations/lightrag.py
index d0e22971..9e135c0f 100644
--- a/backend/package/yuxi/knowledge/implementations/lightrag.py
+++ b/backend/package/yuxi/knowledge/implementations/lightrag.py
@@ -348,6 +348,7 @@ class LightRagKB(KnowledgeBase):
 
             # Check markdown file exists
             if not file_meta.get("markdown_file"):
+                await self._mark_file_unparsed(file_id, operator_id)
                 raise ValueError("File has not been parsed yet (no markdown_file)")
 
             # Clear previous error if any
diff --git a/backend/package/yuxi/knowledge/implementations/milvus.py b/backend/package/yuxi/knowledge/implementations/milvus.py
index 35b82a2d..5ba23cf2 100644
--- a/backend/package/yuxi/knowledge/implementations/milvus.py
+++ b/backend/package/yuxi/knowledge/implementations/milvus.py
@@ -333,6 +333,7 @@ class MilvusKB(KnowledgeBase):
 
             # Check markdown file exists
             if not file_meta.get("markdown_file"):
+                await self._mark_file_unparsed(file_id, operator_id)
                 raise ValueError("File has not been parsed yet (no markdown_file)")
 
             # Clear previous error if any
diff --git a/backend/test/unit/backends/test_lightrag_serialization.py b/backend/test/unit/backends/test_lightrag_serialization.py
index e3de87d8..c6a01982 100644
--- a/backend/test/unit/backends/test_lightrag_serialization.py
+++ b/backend/test/unit/backends/test_lightrag_serialization.py
@@ -52,6 +52,36 @@ async def _fake_read_markdown(*_args, **_kwargs) -> str:
     return "mock markdown"
 
 
+async def test_index_file_marks_file_unparsed_when_markdown_file_is_missing(
+    light_rag_kb: LightRagKB,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    persisted: list[str] = []
+    db_id = "kb_missing_markdown"
+    file_id = "file-missing"
+    light_rag_kb.databases_meta[db_id] = {"metadata": {}}
+    light_rag_kb.files_meta[file_id] = {
+        "status": FileStatus.PARSED,
+        "path": "/tmp/file.md",
+        "filename": "file.md",
+        "processing_params": {},
+    }
+
+    async def fake_persist_file(saved_file_id: str) -> None:
+        persisted.append(saved_file_id)
+
+    monkeypatch.setattr(light_rag_kb, "_persist_file", fake_persist_file)
+    monkeypatch.setattr(light_rag_kb, "_get_lightrag_instance", _make_async_return(SimpleNamespace()))
+
+    with pytest.raises(ValueError, match="no markdown_file"):
+        await light_rag_kb.index_file(db_id, file_id, operator_id="user-1")
+
+    assert light_rag_kb.files_meta[file_id]["status"] == FileStatus.UPLOADED
+    assert "markdown_file" not in light_rag_kb.files_meta[file_id]
+    assert light_rag_kb.files_meta[file_id]["updated_by"] == "user-1"
+    assert persisted == [file_id]
+
+
 async def test_index_file_serializes_writes_within_same_database(
     light_rag_kb: LightRagKB,
     monkeypatch: pytest.MonkeyPatch,
@@ -151,9 +181,15 @@ async def test_add_documents_auto_index_uses_latest_parsed_metadata(monkeypatch:
         ) -> None:
             calls.append(("update_params", file_id))
 
-        async def index_file(self, _db_id: str, file_id: str, operator_id: str | None = None) -> dict:
+        async def index_file(
+            self,
+            _db_id: str,
+            file_id: str,
+            operator_id: str | None = None,
+            params: dict | None = None,
+        ) -> dict:
             calls.append(("index", file_id))
-            return {"file_id": file_id, "status": FileStatus.INDEXED, "operator_id": operator_id}
+            return {"file_id": file_id, "status": FileStatus.INDEXED, "operator_id": operator_id, "params": params}
 
     class FakeTaskContext:
         async def set_message(self, _message: str) -> None:
diff --git a/docs/develop-guides/roadmap.md b/docs/develop-guides/roadmap.md
index 0ea12f66..93bded10 100644
--- a/docs/develop-guides/roadmap.md
+++ b/docs/develop-guides/roadmap.md
@@ -37,6 +37,7 @@
 ### 0.6.2 开发记录
 
 <!-- 0.6.2 的内容请放在这里 -->
+- 修复知识库文档入库状态回退：当已解析文件缺失 `markdown_file` 解析产物时，索引流程会将文件状态恢复为未解析，便于重新解析而不是停留在索引失败。
 - 优化 Agent 输入框文件 mention：用户级 workspace 文件候选改为从独立 workspace API 递归加载，不再依赖 active thread；插入时仍转换为 `/home/gem/user-data/workspace/` 沙盒虚拟路径，并修复附件上传后未立即刷新 mention 候选的问题。
 - 调整知识库思维导图后端结构：将思维导图路由文件重命名为知识库语义更明确的 router，并把文件列表整理、提示词构建、AI JSON 解析等纯逻辑下沉到知识库 utils。
 - 新增个人工作区预览与管理：提供独立于对话 thread 的用户级 workspace API，并增加“工作区”页面，用于浏览个人 workspace 文件、预览 Markdown/文本/代码/图片/PDF；支持新建文件夹、上传文件、下载文件、删除文件/文件夹和多选删除；工作区预览支持 Markdown/TXT 在右侧预览框内切换编辑并保存，其他格式和非工作区预览默认只读；知识库与团队空间入口先展示到占位层级；默认创建 `agents/AGENTS.md`，并在 Agent 执行时将其内容追加到系统提示词。