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Helpful answers
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Sep 12, 2016 9:35 PM in response to car1977by Drew Reece,When you choose to delete a song you should see a dialog…
'Do you want to move the selected song to the Trash, or keep it in the iTunes Media folder?'
[Cancel] [Keep file] [Move to trash]
Choose 'keep file' & the 'reference' should be removed from iTunes but the file should remain in your Library.
That should allow you to prune out the duplicate pointers to the same files.
Obviously, make a backup before you begin if you don't already have one but it should be fine.