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What I've done in the past is add the new book as a new record. Then I strip all the metadata from the new copy. Then use Edit Metadata > Merge > Merge into First Selected Book.
Note that you can't have two copies of the same format. If you want to retain it in the same record, you can put the old one to a compressed archive and add that, but temporarily disable the Archive Extract plugin.
Annotations are tricky though. I think they're based on position so depending on how much the book has changed it might be in the completely wrong place.
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