So it's just the ebook files themselves that are in the wrong place?
What I'd do:
Back up everything first!
This is what I would do. I am not responsible for what you may do.
Move those (and only those) book files that are in the wrong place to another folder somewhere easy to get to (
not in the library folder). In calibre, create a new library and import that folder of books. Now select them and copy them to the old library as theducks described. Merge duplicates as needed.
Once you're back together, back it up again so you have a nice clean current backup of your library.