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I am pretty much completely ignorant about the underlying structure of e-book files (other than they are basically html, I guess).
However, I do just what you are after by using Sigil and then converting over to mobi.
If you use Sigil and mark chapters with it (it's the drop down box in the top left corner) then when you import the resulting e-pub into Calibre and convert, you get the little chapter marks on the Kindle and can skip.
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