Nonetheless re-installed ( cleaning up everything from the previous install) and noticed that the issue that I am reporting is happening when executing the copy and sending to the "background"only .
If you want confirmations for background transfers, uncheck No confirmations for background transfers:
In "Non Background" mode it asks if a directory is already present or not ...
But even then if tramples ( copies over ) any file equally present .
That's a limitation of SCP. Switch to SFTP protocol for better behaviour.