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If you can keep track of all the footnotes and what they are about and which ones are important, maybe you don't actually need to return to them, since apparent;y you know them all already?
I would suggest manually editing the resultant ebook to remove pagebreaks. I do not see calibre changing to no longer generate pagebreaks -- it was a deliberate feature.
Your footnotes should be listed in the end, where all the footnotes are kept. That is kind of the idea, they need to be somewhere or you wouldn't have any. But they will not be on the same page unless you remove the pagebreaks.
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