Something else to think about: Why have footnotes at all? If it is just a source cite, add a bibliography either at the end of each chapter or a comprehensive one at the end of the book. If the footnote is explanatory, determine how important it is. If important, then inciorporate it into the text; if unimportant or mildly important, consider omitting it.
Think of a footnote/endnote like this: You are making love to a beautiful person in the middle of the afternoon and just as you both approach climax, your doorbell is persistently rung, deflating the moment. The moment is lost and is difficult to recapture. The same is true of a footnote that interrupts the reader's concentration, especially one that really only diverts from the primary text.
Perhaps for an ebook you should rethink your pbook.
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