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Well, Sigil shows a ToC in the toc.ncx file. And I was changing the toc with h1, h2 and h3 headers. After "Generate Table of Contents..." I saw my changes in the toc in Sigil and in the epub, when viewing it in Calibre. Of course the changes were not showing in the content toc. Still the content toc kept showing in the mobi conversion. So my conclusion is that the conversion used the content toc in stead of the metadata toc.
Want me to enter a bug report and upload the original ebook?
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