I'm not quite sure. I suspect you will get duplicate entries and when you try to load them on iPod you will get an error mesage saying some files could not be found. They would show up with an exclamation mark and you can then clear them. Going to edit> show duplicate songs in iTunes could help there. On the other hand the software may do this for you .. Let us know!
I don't know how this software works but if it is possible perhaps you might be able to use it on a selection of songs only and if you loose them you will know not to use it on the others. Only as a precaution you understand!
Good luck
