The file is dragged from the client pane to the server pane. A dialog asking whether to reconnect appears. If reconnect is selected on that dialog, the connection is re-established and the file is transferred. There should be a dialog to verify overwriting the file, but there is not.
WinSCP version: 5.9.2
Windows version 7
This is using GUI with 2 pane presentation (I don't know what "Commander" or "Explorer" are).
The preference "Environment - Confirmations - Overwriting of files" is checked.
The preference "Transfer - Background - No confirmations for background transfers" has no effect whether checked or unchecked.