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You have to remember that conversion from PDF to ePUB is cumbersome to say the least. It always will have issues.
Another thing you will have to remember, is that a TOC can be inline or outline. The outline is just like a page. The inline is incorporated and will always be there. Most readers have a special button or option for that. An inline TOC is usually generated by assembling the headers. You can that by opening the ePUB in Sigil and regenerate the TOC.
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