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Somewhat easier might be to copy the library (as you did), then use a file explorer to search for the non-epub format files, select them, and delete them. Now start calibre, point it at the new library, and run check library (library -> library maintenance -> check library). You will see lots of missing formats (no surprise as you deleted them). Check the 'fix' box & push the fix button, and calibre will make the database match what is actually in the library.
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