Perhaps you sho0uld do your editing in the EPUB format.
Despite the ability to actually unpack and edit an AZW3, I still think it makes a lot more sense to do ebook-building in EPUB. I would only touch the AZW3 if it is the master format (purchased from Amazon) and it just needs quick fixes like for spelling or joining a malformed paragraph...
Just convert with calibre when you are done.
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