I’m trying to compile a story to go onto Bookfunnel, to be downloaded onto people’s devices; it’s my reader magnet. However, I’ve found out that while the Kindle iOS app supports the latest mobi format if the document is sent from the Amazon store, if you side load a document, it will only take mobi7, an older format, missing a lot of the formatting power of the newer version. The result is a I lose some of my heading formatting, and also all my paragraph indents. The headings are not big deal, the lack of indents make for one ugly document. Has anyone found a way to get around this, either doing something different with compile, or by some form of external conversion?
Yes, I would say that Amazon’s iOS reader only supports the Mobi format in name, it’s not really worth it for even proofing, let alone for sale. There is a special alternative format that only works in iOS that you need to use, and the only way I know of making it is described in this post.
Dearest Amber, thank you. 
Went through that, and decided to try putting the mobi into Calibre, and exporting back to mobi, and that cleared up the problems with my indents. I’m not sure I can upload an azw file to Bookfunnel as a mobi file, I might try it, but I’m pretty happy right now. Aside from a bit of formatting loss with my headers, the indents are back.
You might also want to check and see if Bookfunnel will take ePub files for everything now. Amazon is switching over to ePub for all of their production stuff, through KDP and even Kindle Previewer now warns you about using Mobi. It may take a while for the rest of the industry to catch up, but I suspect Mobi’s days are numbered.
As for Calibre, yeah I always forget about that. He built his own Mobi generator from scratch, never relying on Amazon’s tools like we do. As Amazon has let KindleGen kind of go to rot, Calibre’s output is probably the best out there these days. I would even consider just using ePub from Scrivener, and using Calibre for conversion.
That is interesting that it works better on the iPhone as well. It kind of confirms my suspicion that the main problem with it is how KindleGen produces both legacy and new formats in one file, and the iOS reader just doesn’t know how to handle that. By default, Calibre’s Mobi converter only generates the legacy version.
It’s not perfect. I lose a bit of formatting still around my headers, and the TOC is a numbered list. BUT… the paragraph indents are there, which makes it much more readable. I’m not sure anyone is going to care about the rest, and at this point, I don’t either. I did try using Bookfunnel’s conversion, but I believe they’re using KindleGen in the background as well, it came up with the problematic formatting as the straight Scrivener output.
Thanks for the help and suggestions.