Can't Erase itunes Duplicates

I had my old external hard drive crash but I had 90% of my itunes on my ipod so I bought a new external hard drive and had someone help me pull the songs from the ipod onto the new external drive. I now have thousands of duplicates in itunes but every time I try to clean it up and start erasing duplicates (both of which work), for whatever reason the remaining song will then no longer work at all, so basically I can't erase any duplicates at all because I then get an exclamation point next to the remaining song. Is there any way I can fix this and get rid of my duplicates? Obviously, it's a big problem because I can't really sync my ipod.

Thanks!