Indesign does a lot of things that aren't 'legal' per the epub spec. I'd recommend opening and saving the file in Sigil before manipulating it with Calibre. In the latest release Sigil added features which looks for all the bad stuff Indesign does and fixes it - although I don't know if handling an Indesign TOC was on that list. Once you've done that you can probably successfully convert using Calibre.
Edit: Sigil probably won't help you in the TOC department, most of the additions there were around embedded fonts:
http://sigildev.blogspot.com/