The easiest to do is to delete the collection directories, and then re-add the them, that will however loose playcounts, ratings and mess up the playlists (if you have any).
So if you need to keep ratings, playcounts and playlists, you can do it with SQL queries.
See:
https://github.com/strawberrymusicplayer/strawberry/wiki/Find-and-delete-duplicates-from-the-collection-database