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Sigil has an excellent TOC Tool. Generally when I add a chapter (section), all I need do is go to the top menu and click on Tools > Table of Contents > Edit Table of Contents and then click on Okay.
My chapter headings are H2, and of course the added chapter is thus tagged. I have the Flight Crew plug-in installed, and after each such alteration I run it to make sure the altered epub validates.
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