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Originally Posted by sun surfer
Thanks again, eschwartz. 
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Sure thing, fire away all you want.
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So, for instance, if you change the metadata with an epub, then convert to mobi, the mobi will contain the metadata you changed but the epub won't?
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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 one book has different formats with different metadata, how can you look at the embedded metadata in the different formats?
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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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This sounds like what I need, and I've found and added them to the toolbar now. It seems like I can use this so I won't have to convert to embed changed metadata.
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That is what it was created for.
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If I use say send to device will it only embed on the copy being sent or will it also embed on the calibre file?
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Just the copy that was exported.
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Here's what's happening with the identifiers- When I download metadata it often provides various identifiers like amazon, etc. However, when I convert, even though the other metadata I'd changed embeds, the identifiers don't and change back to what they were before I'd downloaded metadata (in other words, it erases the ones that had been added).
At least, this seems to be the case. I tested it all by converting, manually moving the new file to a non-calibre location, deleting the book from calibre and adding the new file to calibre as a new book then checking the metadata.
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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?