For kindle just export to EPUB. You’ll need to convert it to MOBI but Amazon has a converter. Results will vary depending upon how well you’ve set up the file and what version of InDesign you’re using.
The reason I am asking the question is that I created a MOBI file, which looked great when viewed with the downloaded Kindle Previewer, but when I submitted it to Amazon, they put it through their own converter, and it then comes up scrambled when viewed with the online Kindle Previewer. I'm asking about the HTML because that is another file format they will accept, and I'm hoping it will survive the conversion process unscathed. Or at least will be in a form that their support people will deal with.
You seem to have a bizarre workflow. A Reflowable text ePub is one continuous document. Get your ePub created properly so it validates then you can easily convert it to a mobi file using the free Kindle Previewer.
By the way, which version of InDesign and OS do you have?
Watch Ann-Marie's EPUB Fundamentals at www.lynda.com. (Get a free trial as a first time subscriber or subscribe for one month.)
4 hours 20 minutes
The basic concept is that you get a working EPUB and you validate it. Then and only then do you convert it to .mobi.
It is worth watching Ann-Marie and learn to do it correctly.