@tarisa
If you have files with only the .opf file then use either the quality check or simply go to the tags browser and and choose (-) on formats. This will show you all the book files without actual books. Then you can simply copy or move them to another library and add your new books to (yet another) library. Keep your main library clean but hold blanks in another library with a final "incoming" library. this way you know if you send the new books to the library without the formats they either will or won't merge, but at least you know which books are empty files and which aren't
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