Alternatively you could
copy them all to an auto-add folder. calibre will delete each ebook as it gets added (hence copying them first).
But again this is the sort of thing that is only really useful as a preventative measure for the future.
...
Perhaps try using the Connect To Folder option, and check for
matching books. (calibre will scan the folder as though it were an ereader device, and read the metadata for all the books then display them in Device View.)
Then add the non-matching books.