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There really is nothing new under the sun here, Sigil-wise. The HTML ToC has always been rebuilt with the current content of the internal ToC (NCX for EPUB2 and NAV for EPUB3) for a long, long time.
Like Kevin, I don't really think there's much of anything that needs to be done. Tweaking the menu to indicate where the HTML ToC gets its data should be more than enough for those who didn't know. And the overwrite warning gives them opportunity to cancel should they so choose.
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