Do you mean that the connection is lost, but WinSCP notices that only after you try to upload the file?
When I upload a file that already exists in the directory on the server, WinSCP asks me if I want to overwrite the file. So far so good. But if my connection was lost since my last upload, WinSCP asks me to reestablish the connection. But once the connection is re-established, WinSCP just overwites the file in question without asking me if I want to overwrite it!
Using WinSCP 5.7.7 (build 6257) on Windows 7 Pro SP1.