Truth be told, I've bought
more than one ebook as AZW (Kindle format) that came with certain formatting/TOC/chapter marker issues; wherein my best method of fixing it was to convert from AZW to ePUB, fix said issues in Sigil (which was amazingly simple) and convert ePUB to MOBI.
More than once, converting mobi(azw, same thing) -> epub -> mobi
solved problems, whereas I'm not aware of any significant problems that it
created for me at all.
Here's an example:
I have a book that only shows 4 chapter markers; there are more which are hidden, but still don't account for all chapters.
Simply converting in Calibre, whether azw->mobi or azw->epub->mobi, created a book in which the TOC only had a few/some of the chapters listed (depending on whether I had heuristics enabled) but never all of them.
Converting to ePub, opening in Sigil, verifying TOC with its TOC Editor, saving and converting back to mobi FIXED these problems and now I have a nice, clean and pretty TOC with plenty of visible chapter markers at the bottom, all of which are in the right places, with which to easily navigate my book.
Converting between epub and mobi
solves problems, moreso than creates them.