Just use MOBI as long as it continues to work. Maybe amazon will fix their EPUB intake process, but it seems rather unlikely. Once MOBI stops working you can employ the following "trick" to get amazon to accept your EPUBs.
Convert the EPUB to MOBI in calibre, then convert the MOBI back to EPUB. This will cause you to lose all advanced formatting, fonts, etc in the EPUB. But it will result in an EPUB amazon is much more likely to accept in their brain dead email service.
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