I don't have a problem with duplicate books yet

I'm trying to avoid it
I'm downloading a bunch of fanfictions from Fanfiction.net and have a back-up archive on a back-up harddrive. When I add new books to the Back-up harddrive it just makes duplicates of everything instead of overwriting if the info is the same, is it possible there is a plug-in to save me the trouble of having to look through all 1000+ stories? Or maybe some other function?