Thanks eschwartz. You seem to be right: if I convert an EPUB with Kindle Previewer, the resulting MOBI does indeed have the table of contents preserved. For some unknown reason this TOC does not appear in the Kindle Previewer emulation of a Kindle, but if you "side load" the MOBI to an actual Kindle device or to the PC Kindle App, then you will see the TOC. Not sure why Amazon has this bug in the Kindle Previewer.
So, given that the TOC is not in fact destroyed in a Kindlegen EPUB-to-MOBI conversion,m I may indeed use this method of making MOBIs in any cases where Calibre gives me too much trouble. For now I am generally content with the files Calibre makes, so I'm not going back to redo my old EPUB-to-MOBI conversions.
And, as you mention in passing the KindleGen made files are "double MOBI" files that are twice as big, and thus less convenient than the single MOBI files Calibre makes...this matters for offering as downloads off my own site.
kovidgoyal, I don't have a sample EPUB file with ul and li generated bullets to show you the double bullets problem just now. If I am get this situation again, I'll post sample code here. For now I'm just going with the InDesign export fix of exporting bullet lists in paragraph formatting, with my own epubtext-bulleted format on the paragraphs, and letting my epub-bulleted format do the indenting in the ebook. I've never liked the ul and li HTML tags anyway!
