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One way would be to make a separate last file or chapter which holds all the footnotes, and then have the popups display them from there - just name it Footnotes (or Endnotes, if you prefer). That's the way I usually do it when I format pop-up footnotes - it will still appear if browsing page-by-page, but since it's its own separate chapter at the end of the book, it doesn't break the flow.
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