If you've cleaned up your iTunes library using Duplicate Cleaner you may notice that the tracks are still shown there upon starting iTunes.  This is because even though they have been deleted from the hard drive they are still in the iTunes database.  If you try and click to play on one of the removed songs it will fail because the file has gone.

You could remove these 'dead' songs from your library by hand but it could take a long time. The fastest way to it is to use a script - handily Apple provide one.

1. Download the RemoveDeadTracks script here.
2. Unzip the script somewhere (ideally in your documents folder)
3. Close iTunes
4. Double click the RemoveDeadTracks.js file to run the script

iTunes will now open and start removing the dead tracks. You may not notice anything happening and it could take a little while depending on the size of your library. If you look in Song view, you should see the 'items' count reduce at the bottom of the window.