[DiapDealer]

So - this is the source material? Or a combination of source and binary file?

Any part of the MOBI that can be accessed using an archive tool (Springy, WinZip, etc..) is the source... and nothing but the source.

So are you telling me that if I make changes in the .mobi html - or for that matter, in the epub html - and save them, they will not be reflected in the uploaded file unless I generate a new file - no, wait, then I'd have to simply go back to the indd file and do the changes there?

That's exactly what I'm suggesting. Modifying the (x)html source that's included in some MOBI files doesn't alter the MOBI itself one bit.

Edit source... then rebuild the MOBI (whether that rebuild is done with the indd plugin, kindlegen, mobipocket creator, or whatever). That's how MOBIs are altered: change the source.... rebuild the MOBI... each time. You can't modify them on the fly.