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You can, however, use KindleUnpack (there is a plugin that incorporates this into calibre) to split the hybrid MOBI in two, and calibre will be able to properly update the AZW3 or MOBI components, individually.
(MOBI should only ever be used on a device that doesn't support AZW3. Basically, the Kindle DX/2/Original. It is a pity that kindlegen doesn't support choosing your output format, and bundling KindleUnpack with KCC would be going a little overboard.)
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