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Create a new, empty library.
Select all the books in your current library (not in the library folder, but in the GUI), right-click and select "copy to library" (choose that new library you just created) -> delete after copy.
Wait until all the books have been copied to the new library. Your current library list should now be empty.
Now look in the library folder. There should be some files there that weren't in the Calibre database.
Switch to the new library where you copied all your books, and use the "add books" button to add all the leftover files in the old library folder.
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