When you don't select overwrite, the song restore should skip that song, but if you do, it should overwrite the song. The fact that there are numbers being appended means that there is some permission issue with the file - this shouldn't be happening and I'll look into it. This method does not check for last edit dates, etc.
Actually, there is a smarter way to synchronise songs and sets between your devices:
Alternatively, use a separate app such as Drivesync or Dropsync to keep your entire OpenSongApp content (everything in the OpenSong folder including pads, songs, sets, etc):