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Please ignore JSWolf's weird and incorrect advice. There's no need to abandon your old library.
Just remove the DRMed format (usually will be "AZW" format), and re-import the book into the calibre entry for the book. There's no need to delete the entire record.
As for finding them, you should be able to sort your library by import date, and so find the books that were imported when the DRM removal was broken.
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