Kobo has support to bounce back and forth between two locations in the book, and this is normally how I manage footnotes. Normally I only read one book at a time and this has been working for me, however...
I've recently been reading a few books at once (life's like that at the moment), including two with endnotes, and I discovered that Kobo doesn't save this page bounce thing when you leave the current read. So every time I returned I had to set up the footnotes location again. A relatively minor annoyance in the scheme of things, but definitely annoying.
P.S. I got in the habit of loading my Kobo with epub files. When I tried kepub several years ago I didn't much like it, neither the footnote nor image features seemed very smooth, but it's possible that has improved since then, I probably should try.
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