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If you just want to delete the now empty entries, and a) they don't contain info you specifically want to merge into the entry you kept, and b) those entries now contain no formats (that is, no book files) c) you don't have other arbitrary book entries with no formats, then you can just search for 'formats:false'
If any of a through c are the case, you'll need to probably either do it manually, or somehow mark those and exclude them. Or perhaps search by date modified? Something like 'formats:false and last_modified:=today' (or whatever date you run the find duplicates).
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