In moving my music onto a new computer, I copied my backup music folder, which contained my iTunes library definition, onto my new drive. Then when I installed iTunes, I had duplicate entries of each file, with one being a bad link (as the path was different on my new computer). With nearly 4000 files (8000 listed), I didn't want to manually go through my list and delete the Songs that were broken (Exclamation point next to the Name in iTunes.)
Fortunately with some searching, I found Paul Mayne, who had a solution. Through the use of 2 Smart Play Lists and a Play List, I was able to quickly remove the dead, duplicate listings. See Paul's post for the specific details.
You can may also find yourself in trouble if you let iTunes scan your backup drive and your primary drive. This would actually create duplicates, one pointing to each drive. To correct this, temporarily rename the music folder on your back drive, which will make all the listings on the backup drive to now have invalid links. Then use Paul's technique to remove the invalid listings. Finally, rename the backup drive music folder back to what it was.