Segue:
Manual Solution:
1. Use iTunes built-in “Find Duplicates” feature to find and remove the duplicate tracks in iTunes – this doesn’t affect your drive yet).
2. Highlight every track in your iTunes Library (still in iTunes, not on your drive) and then drag the tracks from iTunes to a new Folder on your drive.
3. This will make a complete copy of your Library (without any duplicates)
4. Delete every track in iTunes and every file in your original Library on your drive.
5. Then, either move the contents of your new Folder to your Library folder and drop the Library Folder back into iTunes, or just tell iTunes that your Library has moved to the new Folder.
You’ll now have a new Library with no duplicates.