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I also use koreader to read a fair number of non-fiction books with footnotes. One of the tweaks I make when pulling a new book into Calibre is making sure the book's footnote class name (if it has footnotes) matches one of those class names koreader supports.
IIRC, I've seen a book like this before, where a few multi-paragraph footnotes had paragraphs that were "siblings" - instead of children - to the first paragraph, with the correct class name, and so koreader would only show the first paragraph at the bottom of the page.
I think I "fixed" this by just hand editing those few footnotes with multiple paragraphs to be one big html paragraph, with the correct class name.
As an aside, I have my Calibre library in Linux and koreader has Linux builds (not sure about windows), so I can actually open a book in koreader from Calibre and test it. Fixing footnotes is the one thing I do with new books in Calibre that I test this way.
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