Originally Posted by mrmikel
Hitch, who involved in conversions, has pointed out that the new epub standard will all but require an HTML TOC, so even if you strip it out for now, it might be worthwhile saving a version with it in it.
ePub 3 has some specific requirements for TOC that are not met by an Inline TOC today. It needs semantics not available in 2.1 thus there is no reason to think keeping one is important today. Sigil can generate one automatically at any time that it might be needed.