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So, from what I understand, you want to use the inline TOC as metadata TOC? To do that, you need to tell Calibre to look for chapter headings via the structure detection part of the conversion settings. It will then add the headings it finds to a metadata TOC. As far as I know, there's no direct way to use the inline TOC as metadata TOC in Calibre. You might have some luck with the Mobipocket Creator, or, if you want to convert some more, Sigil (you'd have to create an ePub, edit that to your liking and convert to Mobi).
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