I've lost a file a couple of times already due to the fact that if renaming a file with the name of an existing file, Cyberduck offers to rewrite the other file. Since those confirmations are pretty routine in everyday computer use, I just click yes automatically only to discover I've lost the other file for good. There is no way to disable that "feature" either so I'd say it's a usability bug/annoyance that can cause major headaches.