I have an ID document such as it restarts footnote's numbering in every Section. And it works OK except when I export the reflowable EPUB. Then, footnotes numbering are continous, with no restarting anywhere at all.
There is actually a solution that avoids this annoying manual editing, not an option for most users. It's about working with InDesign Books, every chapter being a document inside that book. This way restarting of footnotes per chapter is perfectly possible when exporting the EPUB.
Not the best, but as long as it seems Adobe doesn't care much about it, I don't expect they'll fix that anytime soon.