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Originally Posted by eschwartz
Correct. In fact, it would be more correct to say you changed the metadata for the book record, not the EPUB attached to the book record.
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If you are changing the metadata for the book record it sounds like it should change it for all formats of that book but it doesn't so what am I missing here?
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You can look at the metadata a couple ways.
You can use the command-line tool `ebook-meta`, but I think we'll skip that one. 
You can edit the book (if EPUB or AZW3) and look at the OPF. In XML. I think we'll skip that one too.
Winner:
You can open the book in the calibre ebook-viewer (View --> Choose format), and use the toolbar option "Show book metadata".
You can also just use Embed metadata to make sure it's up to date.
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Yes, the winner is more up my alley, thanks.
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On second thought, I believe identifiers is one of the things MOBI/AZW3 just doesn't really support.
EPUB, on the other hand, supports arbitrary custom metadata types.
Was this an AZW3?
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Yep. That's probably it then. It only seems to keep isbn and mobi-asin and deletes the rest, even the Amazon identifier. The Quality Check plug-in that you suggested will embed the Amazon identifier though, if I've already added it to the metadata, as the mobi-asin.