I still think that epub3 apps with built-in popup footnote support is the easiest way to handle this issue.
For testing purposes I looked into loading footnote definitions via jQuery
.load(), but it only worked with the desktop version of
ADE 4.5 and the Android version of
Gitden Reader. (Unlike my
first version, it doesn't work with Sigil, which is usually a bad sign.)
If you want to test this but have neither ADE 4.5. nor Gitden Reader for Android installed, simply unpack the epub and open the chapter files with a Web browser.
The code does the following:
1. It populates an empty div at the end of the chapter with a footnote definition loaded via the target id from an endnotes html file. (This part worked with most readers that support JavaScript.)
2. When the user selects the backlink it deletes the definition from the div and goes back to the footnote reference. (That part didn't work with all readers, however, it's quite possible that there's a bug in my very simple JavaScript code.)
(It should be possible to adapt my code so that it displays the div as a popup footnote, but I lack the skills to do it. Also it'd most likely duplicate the existing popup footnote function.)