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Way too many ways to embed the wrongness before you can run your test.
Conversion, Polish, Embed Metadata, Modify EPUB (PI)...
The big Q is how you managed this? Were you using the Read from Filename metadata option (and the chosen template was wrong)?
Did you do a Bulk Metadata download? (without ISBN or similar, I've seen Calibre get wrong results. I always cherry pick from the returned choices, manually nowadays)
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