You could also consider moving footnotes inline,
Could you explain a little more, please?
Maybe some CSS if appropriate.
We torture ourselves too much in attempts to copy printed layout rather than designing efficient ebooks.
Everything I do with Sigil and Calibre (both GREAT programs) is pretty much just for myself and family to make (very) poorly converted PD books into something readable on the Kindles.
The 'back and forth' linking for footnotes is tedious, and sometimes I'm not careful enough
If by 'inline' you mean click it and it expands (displays) in location and then click it and it 'shrinks' that's be a lot easier that manually doing all the footnotes manually