diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b0f43ed42..bd91d3895 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -44,6 +44,12 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+  ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+  STORE_API_KEY: ${{ secrets.STORE_API_KEY }}
+  TAVILY_API_KEY: ${{ secrets.TAVILY_API_KEY }}
+
 jobs:
   check-nightly-status:
     name: Check PyPI Version Update
diff --git a/.github/workflows/python_test.yml b/.github/workflows/python_test.yml
index 9fb41a4ba..660ce99bc 100644
--- a/.github/workflows/python_test.yml
+++ b/.github/workflows/python_test.yml
@@ -33,6 +33,8 @@ env:
   POETRY_VERSION: "1.8.2"
   NODE_VERSION: "21"
   PYTEST_RUN_PATH: "src/backend/tests"
+  OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+  ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
 
 jobs:
   build:
@@ -69,6 +71,8 @@ jobs:
           max_attempts: 2
           command: make unit_tests args="-x -vv --splits ${{ matrix.splitCount }} --group ${{ matrix.group }} --reruns 5"
 
+
+
   integration-tests:
     name: Integration Tests - Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
diff --git a/src/backend/base/langflow/api/v2/files.py b/src/backend/base/langflow/api/v2/files.py
index 391e0e2ce..879ff015d 100644
--- a/src/backend/base/langflow/api/v2/files.py
+++ b/src/backend/base/langflow/api/v2/files.py
@@ -11,7 +11,8 @@ from zoneinfo import ZoneInfo
 
 from fastapi import APIRouter, Depends, File, HTTPException, UploadFile
 from fastapi.responses import StreamingResponse
-from sqlmodel import String, cast, col, select
+from loguru import logger
+from sqlmodel import col, select
 
 from langflow.api.schemas import UploadFileResponse
 from langflow.api.utils import CurrentActiveUser, DbSession
@@ -112,35 +113,36 @@ async def upload_user_file(
 
     # Create a new database record for the uploaded file.
     try:
-        # Enforce unique constraint on name
-        # Name it as filename (1), (2), etc.
-        # Check if the file name already exists
+        # Enforce unique constraint on name, except for the special _mcp_servers file
         new_filename = file.filename
         try:
             root_filename, _ = new_filename.rsplit(".", 1)
         except ValueError:
             root_filename, _ = new_filename, ""
 
-        # Check if there are files with the same name
-        stmt = select(UserFile).where(cast(UserFile.name, String).like(f"{root_filename}%"))
-        existing_files = await session.exec(stmt)
-        files = existing_files.all()  # Fetch all matching records
+        # Special handling for the MCP servers config file: always keep the same root filename
+        if root_filename == MCP_SERVERS_FILE:
+            # Check if an existing record exists; if so, delete it to replace with the new one
+            existing_mcp_file = await get_file_by_name(root_filename, current_user, session)
+            if existing_mcp_file:
+                await delete_file(existing_mcp_file.id, current_user, session, storage_service)
+        else:
+            # For normal files, ensure unique name by appending a count if necessary
+            stmt = select(UserFile).where(col(UserFile.name).like(f"{root_filename}%"))
+            existing_files = await session.exec(stmt)
+            files = existing_files.all()  # Fetch all matching records
 
-        # If there are files with the same name, append a count to the filename
-        if files:
-            counts = []
+            if files:
+                counts = []
 
-            # Extract the count from the filename
-            for my_file in files:
-                match = re.search(r"\((\d+)\)(?=\.\w+$|$)", my_file.name)  # Match (number) before extension or at end
-                if match:
-                    counts.append(int(match.group(1)))
+                # Extract the count from the filename
+                for my_file in files:
+                    match = re.search(r"\((\d+)\)(?=\.\w+$|$)", my_file.name)
+                    if match:
+                        counts.append(int(match.group(1)))
 
-            # Get the max count and increment by 1
-            count = max(counts) if counts else 0  # Default to 0 if no matches found
-
-            # Split the extension from the filename
-            root_filename = f"{root_filename} ({count + 1})"
+                count = max(counts) if counts else 0
+                root_filename = f"{root_filename} ({count + 1})"
 
         # Compute the file size based on the path
         file_size = await storage_service.get_file_size(
@@ -462,24 +464,26 @@ async def delete_file(
 ):
     """Delete a file by its ID."""
     try:
-        # Fetch the file from the DB
-        file = await fetch_file_object(file_id, current_user, session)
-        if not file:
+        # Fetch the file object
+        file_to_delete = await fetch_file_object(file_id, current_user, session)
+        if not file_to_delete:
             raise HTTPException(status_code=404, detail="File not found")
 
         # Delete the file from the storage service
-        await storage_service.delete_file(flow_id=str(current_user.id), file_name=file.path)
+        await storage_service.delete_file(flow_id=str(current_user.id), file_name=file_to_delete.path)
 
         # Delete from the database
-        await session.delete(file)
+        await session.delete(file_to_delete)
         await session.flush()  # Ensures delete is staged
-        await session.commit()  # Commit deletion
 
+    except HTTPException:
+        # Re-raise HTTPException to avoid being caught by the generic exception handler
+        raise
     except Exception as e:
-        await session.rollback()  # Rollback on failure
+        # Log and return a generic server error
+        logger.error("Error deleting file %s: %s", file_id, e)
         raise HTTPException(status_code=500, detail=f"Error deleting file: {e}") from e
-
-    return {"message": "File deleted successfully"}
+    return {"detail": f"File {file_to_delete.name} deleted successfully"}
 
 
 @router.delete("")
diff --git a/src/backend/base/langflow/api/v2/mcp.py b/src/backend/base/langflow/api/v2/mcp.py
index 301b017a0..84e18bbdf 100644
--- a/src/backend/base/langflow/api/v2/mcp.py
+++ b/src/backend/base/langflow/api/v2/mcp.py
@@ -1,3 +1,4 @@
+import contextlib
 import json
 from io import BytesIO
 
@@ -43,8 +44,22 @@ async def get_server_list(
     # Read the server configuration from a file using the files api
     server_config_file = await get_file_by_name(MCP_SERVERS_FILE, current_user, session)
 
-    # If the file does not exist, create a new one with an empty configuration
-    if not server_config_file:
+    # Attempt to download the configuration file content
+    try:
+        server_config_bytes = await download_file(
+            server_config_file.id if server_config_file else None,
+            current_user,
+            session,
+            storage_service=storage_service,
+            return_content=True,
+        )
+    except (FileNotFoundError, HTTPException):
+        # Storage file missing - DB entry may be stale. Remove it and recreate.
+        if server_config_file:
+            with contextlib.suppress(Exception):
+                await delete_file(server_config_file.id, current_user, session, storage_service)
+
+        # Create a fresh empty config
         await upload_server_config(
             {"mcpServers": {}},
             current_user,
@@ -52,24 +67,23 @@ async def get_server_list(
             storage_service=storage_service,
             settings_service=settings_service,
         )
+
+        # Fetch and download again
         server_config_file = await get_file_by_name(MCP_SERVERS_FILE, current_user, session)
+        if not server_config_file:
+            raise HTTPException(status_code=500, detail="Failed to create _mcp_servers.json") from None
 
-    # Make sure we have it now
-    if not server_config_file:
-        raise HTTPException(status_code=500, detail="Server configuration file not found.")
+        server_config_bytes = await download_file(
+            server_config_file.id,
+            current_user,
+            session,
+            storage_service=storage_service,
+            return_content=True,
+        )
 
-    # Download the server configuration file content
-    server_config = await download_file(
-        server_config_file.id,
-        current_user,
-        session,
-        storage_service=storage_service,
-        return_content=True,
-    )
-
-    # Parse the JSON content
+    # Parse JSON content
     try:
-        servers = json.loads(server_config)
+        servers = json.loads(server_config_bytes)
     except json.JSONDecodeError:
         raise HTTPException(status_code=500, detail="Invalid server configuration file format.") from None
 
diff --git a/src/backend/tests/unit/api/v2/test_files.py b/src/backend/tests/unit/api/v2/test_files.py
index 599604b5a..3a8154052 100644
--- a/src/backend/tests/unit/api/v2/test_files.py
+++ b/src/backend/tests/unit/api/v2/test_files.py
@@ -187,7 +187,7 @@ async def test_delete_file(files_client, files_created_api_key):
 
     response = await files_client.delete(f"api/v2/files/{upload_response['id']}", headers=headers)
     assert response.status_code == 200
-    assert response.json() == {"message": "File deleted successfully"}
+    assert response.json() == {"detail": "File test deleted successfully"}
 
 
 async def test_edit_file(files_client, files_created_api_key):
diff --git a/src/backend/tests/unit/api/v2/test_mcp_servers_file.py b/src/backend/tests/unit/api/v2/test_mcp_servers_file.py
new file mode 100644
index 000000000..9a68bcbd3
--- /dev/null
+++ b/src/backend/tests/unit/api/v2/test_mcp_servers_file.py
@@ -0,0 +1,164 @@
+import io
+import uuid
+from types import SimpleNamespace
+from typing import TYPE_CHECKING
+
+import pytest
+from fastapi import UploadFile
+
+# Module under test
+from langflow.api.v2.files import MCP_SERVERS_FILE, upload_user_file
+
+if TYPE_CHECKING:
+    from langflow.services.database.models.file.model import File as UserFile
+
+
+class FakeStorageService:  # Minimal stub for storage interactions
+    def __init__(self):
+        # key -> bytes
+        self._store: dict[str, bytes] = {}
+
+    async def save_file(self, flow_id: str, file_name: str, data: bytes):
+        self._store[f"{flow_id}/{file_name}"] = data
+
+    async def get_file_size(self, flow_id: str, file_name: str):
+        return len(self._store.get(f"{flow_id}/{file_name}", b""))
+
+    async def delete_file(self, flow_id: str, file_name: str):
+        self._store.pop(f"{flow_id}/{file_name}", None)
+
+
+class FakeResult:  # Helper for Session.exec return
+    def __init__(self, rows):
+        self._rows = rows
+
+    def first(self):
+        return self._rows[0] if self._rows else None
+
+    def all(self):
+        return list(self._rows)
+
+
+class FakeSession:  # Minimal async session stub
+    def __init__(self):
+        self._db: dict[str, UserFile] = {}
+
+    async def exec(self, stmt):
+        # Extremely simplified: detect by LIKE pattern or equality against name/id
+        # We only support SELECT UserFile WHERE name LIKE pattern or id equality
+        stmt_str = str(stmt)
+        if "user_file.name" in stmt_str:
+            # LIKE pattern extraction
+            pattern = stmt_str.split("like(")[-1].split(")")[0].strip('"%')
+            rows = [f for name, f in self._db.items() if name.startswith(pattern)]
+            return FakeResult(rows)
+        if "user_file.id" in stmt_str:
+            uid = stmt_str.split("=")[-1].strip().strip("'")
+            rows = [f for f in self._db.values() if str(f.id) == uid]
+            return FakeResult(rows)
+        return FakeResult([])
+
+    def add(self, obj):
+        self._db[obj.name] = obj
+
+    async def commit(self):
+        return
+
+    async def refresh(self, obj):  # noqa: ARG002
+        return
+
+    async def delete(self, obj):
+        self._db.pop(obj.name, None)
+
+    async def flush(self):
+        return
+
+
+class FakeSettings:
+    max_file_size_upload: int = 10  # MB
+
+
+@pytest.fixture
+def current_user():
+    class User(SimpleNamespace):
+        id: str
+
+    return User(id=str(uuid.uuid4()))
+
+
+@pytest.fixture
+def storage_service():
+    return FakeStorageService()
+
+
+@pytest.fixture
+def settings_service():
+    return SimpleNamespace(settings=FakeSettings())
+
+
+@pytest.fixture
+def session():
+    return FakeSession()
+
+
+@pytest.mark.asyncio
+async def test_mcp_servers_upload_replace(session, storage_service, settings_service, current_user):
+    """Uploading _mcp_servers.json twice should keep single DB record and no rename."""
+    content1 = b'{"mcpServers": {}}'
+    file1 = UploadFile(filename=f"{MCP_SERVERS_FILE}.json", file=io.BytesIO(content1))
+    file1.size = len(content1)
+
+    # First upload
+    await upload_user_file(
+        file=file1,
+        session=session,
+        current_user=current_user,
+        storage_service=storage_service,
+        settings_service=settings_service,
+    )
+
+    # DB should contain single entry named _mcp_servers
+    assert list(session._db.keys()) == [MCP_SERVERS_FILE]
+
+    # Upload again with different content
+    content2 = b'{"mcpServers": {"everything": {}}}'
+    file2 = UploadFile(filename=f"{MCP_SERVERS_FILE}.json", file=io.BytesIO(content2))
+    file2.size = len(content2)
+
+    await upload_user_file(
+        file=file2,
+        session=session,
+        current_user=current_user,
+        storage_service=storage_service,
+        settings_service=settings_service,
+    )
+
+    # Still single record, same name
+    assert list(session._db.keys()) == [MCP_SERVERS_FILE]
+
+    record = session._db[MCP_SERVERS_FILE]
+    # Storage path should match user_id/_mcp_servers.json
+    expected_path = f"{current_user.id}/{MCP_SERVERS_FILE}.json"
+    assert record.path == expected_path
+
+    # Storage should have updated content
+    stored_bytes = storage_service._store[expected_path]
+    assert stored_bytes == content2
+
+    # Third upload with server config provided by user
+    content3 = (
+        b'{"mcpServers": {"everything": {"command": "npx", "args": ["-y", "@modelcontextprotocol/server-everything"]}}}'
+    )
+    file3 = UploadFile(filename=f"{MCP_SERVERS_FILE}.json", file=io.BytesIO(content3))
+    file3.size = len(content3)
+
+    await upload_user_file(
+        file=file3,
+        session=session,
+        current_user=current_user,
+        storage_service=storage_service,
+        settings_service=settings_service,
+    )
+
+    stored_bytes = storage_service._store[expected_path]
+    assert stored_bytes == content3