Thanks for your report. Will take a look.
If a file that already exists on a server is transferred from client to server via SCP on a stale connection (after the server has rebooted) there is no prompt to verify the overwrite (after reconnection) as normally occurs.
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.