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I've done some testing and the way to get single footnote with Calibre generated azw3 is to add "page-break-before:always" to CSS. Which would look awful for book with lots of footones. So I will be using Kindlegen for book that have more than 5 footnotes.
Also while testing I noticed that if you markup your footnotes with href first id second but in seperate a tags then for both Kindlegen and Calibre generated azw3 file clicking on footnote number works "the old way", it jumps to the endnotes html file instead of opening a popup window.
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