It sounds like you didn't copy the files to the PC, but instead indexed (just scanned) them. In that case they're lost.

I transfered all the files from the ipod to mediamonkey but have since wiped the ipod's data. I files on media monkey are still sourced to the ipod directory, they did not transfer to a new folder in my computer. Is there a way to move these files to a new folder now, or have these files been lost? I can see all the files in my library, they are not playable though.