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I have TOC in all my Mobi books (and it's my main format). From this I convert to ePub and lit with Calibre, and it keeps the TOC (if it doesn't it, usually the option "--use-auto-toc" is OK). The only problem with ePub is that the book shows the contents as another "chapter" into the book. You can remove it manually, but if you want to make a batch convert, you must take this into account.
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