Deletion is a drastic step which may be difficult for a novice to recover from.
I suggest an option (preferably the default option) of Deletion to the Recycle Bin,
and a pop-up or alternative notice advising to NOT empty the bin until after rebooting and checking that the duplicates really are redundant before emptying the bin.
Or maybe use a method similar to the registry cleaner. Offer to make backups, store them in a user designated folder to be deleted when everything still works.