Create a new empty library. Select all books in the current library, right click, copy to library (delete after copy)
that will move all books calibre is tracking into your new library. Now switch tot he new library. Then you can either discard the old library folder if it contains only duplicates, or add the books from it by right clicking the add books button and choosing "Add books from directories, one book per directory" and choosing the old library folder.
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