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I'm sorry I can't help, Knuckles. I don't have a Kindle and only ever convert the other way, i.e. MOBI to EPUB or sometimes MOBI to HTML to EPUB using Calibre. I know the MOBI format isn't as flexible as EPUB but I wasn't aware that the format got trashed when going from EPUB to MOBI in Calibre.
If you have the HTML and you have experience editing it in a text editor, you can manually edit the chapter headings to have <h1>, <h2> etc tags. Then you can recreate the TOC using Calibre Convert - Structure Detection/Table of Contents settings during a HTML (zipped) to MOBI conversion.
What do your Chapter headings currently look like in the HTML file you created?
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