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@johnnyb: Nothing in life in certain, especially software behavior.
The only thing that is known concerning the whole "system" is that what will get stored on Amazon servers and what will get delivered is dependent on whole set of Kindle devices and Kindle apps that are associated with that particular account.
If you only have couple of Kindle eInk devices that both support KF8 then Amazon will PROBABLY store on its servers just the KF8 portion of the dual mobi file you've sent. If you also have say Kindle 2 registered to that same Amazon account.. it has to store "dual mobi" to be able to deliver correct format to all your devices.
I admit that I don't really use Amazon's Personal Documents Archive service BUT those time I've tested it with dual mobi files (I wanted to check the same thing, will delivered KF8 portion of the book have soft hyphens) it always deliver azw3 file to my Kindle.
When I was testing the hyphens thing I happened to also test embedded fonts and choose Calibre's option to subset used font, and ended-up with azw3 book which had squares in place of soft hyphens if I enable "Publisher font" (it was obviously missing that font character.. so I concluded that Calibre probably did font subsetting based on "old mobi" portion which did't have soft hyphens).
So yes, hyphenated epub> convert to mobi "both">e-mail it works. You get hyphenated azw3. And if it was possible to then (post download) USB-sideload .apnx files (for page numbers) and cover thumbnails maybe I would give more serious consideration to email instead of USB-sideload my books, especially now that newer Kindle firmware doesn't use that ugly "personal" banner on bottom of cover thumbnails.
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