After consolidating your iTunes library you may find that many of the songs had the little exclamation mark icon that means "this file is not where it was when it was added to the library" because you'd made changes to your music folder for organization purposes. But iTunes offers no easy way to get rid of the files that have those errors.
To get rid of them edit all of the music files (select all in the music tab) in the Comment tag to "I exist." Then I made a custom playlist that found songs that did NOT have "I exist" as their comment. This created a list that contained all the missing files (because you can't change tags on files that don't exist). I selected all and shift+delete and deleted them from the library.
No more missing files.
I.T. Tips from fergus.it