I wrote you a direct message with the debug output.
concerning the overwrite behaviour, I think a solution might be as follows. Whenever a downloaded project file name clashes with an existing file a pop-up window appears to ask whether the file should be skipped or overwritten, and the window has a checkbox “apply the same action to all files”. I think this gives user enough control without landing him in a situation where they need to click through hundred boxes to complete a backup.