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Are you asking about Reflowable EPUB or Fixed Layout EPUB? EPUB 2 or EPUB 3? The answers are probably different depending on which you're talking about?
Reflowable, EPUB 3. Thanks.
Bump. Anybody got anything on this?
It seems not to be something the regulars who visit here know about.
Did you try doing it?
Not yet. I was hoping to get some advice first. But since there doesn't appear to be any, I shall blaze my own trail and report back!
Welp, this project finally made its way back to the top of my to-do list, so I can now report back on how it worked. The footnotes work like footnotes should. The endnotes, alas, work like plain text -- the reference number is there, but it does not link to the note. So...bummer. Lotsa extra work needed to convert all ~600 of them back to footnotes.
I have tested the new feature endnotes, but the links didn't work in epub files, when you divide the indd files by export. Because the link <a href> don't get all path from file, only the anchor #.
But regular footnotes from Indd works as endnotes, because always goes to the end of chapter. If you want all the notes at the end of eBook, you export without divide the file, then all footnotes goes at the end.
Open the epub in Sigil and divide the chapter from Menu Edit > Split at cursor. This way is possible keep the links working