I gave you advice via pm. Check both iPod extraction back to iTunes AND manually updating your iPod instead of automatic updating. How to transfer music to my iPod (& iTunes) - for video

The other file recovery program is Restoration (click on link)

But you may need to close down applications whilst you're running it. Also, when recovering files, don't save them back to where you are recovering them or you'll copy over others that aren't yet recovered; ie: choose another partition or external device to save to.