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So if you do as I suggest and the paragraphs used as footnotes are not too long and not heading level (body text type in the wordprocessor style) then if the epub2 is exported by Calibre as a kepub using the Kobo Extended Driver (or maybe even just renamed), then automagically the footnotes will be popup footnotes, but linked pages where the anchor/bookmark is at the start of a heading or a large paragraph will be just navigation.
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