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When working with ePUbs there is the "original epub" that stays as well, but maybe that's just for ePub? Either way I like this workaround:
Create a separate library for book to convert. Copy the book to it (keep it in the main library as well), fiddle around with it until your happy. Should all go horribly wrong, delete from the conversion library and copy it once again.
Once you're happy, remove it from the main library and then bring your converted copy there.
It doesn't solve the "merge" thing though...
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