When you copy a file to the host which already exists on the host, you are normally presented with a popup stating the file already exists, and how do you want to handle it? Overwrite, rename, etc.
However, if the session has been lost by the host but WinSCP has not gone into reconnect process yet when you make this copy request, it sits in transfer, pops up it can't connect to the host so I abort, then it presents me with a reconnect box, and once that connection is made the file is transferred without notifying me about the existing file and asking how to handle it.
I have version 5.2.1, Build 3231. It has always worked this way in the years that I have been using it.