Sadly, as everyone mentioned, the only way you can currently do this is "by hand". Feel free to PM me the EPUB, and I can see what I can do with the code on my end.
This is a problem I ran into many months ago, and I made myself a custom program to handle it. (it is hideous code and buggy (I have to pre-clean the code before I feed it in) and I would rather not let people see the horror.
It reads in an HTML file, and starts counting from 1. Every <sup>###</sup> it hits, it generates a pointer link:
<a href="#fn1" id="ft1"></a>
Then iterates by 1.
Once my code hits an "<hr />" (Which I use at the end of every HTML file to denote a footnote section). It starts iterating from 1 again, and every <sup>###</sup> it hits, it replaces it with the opposite link:
<a href="#ft1" id="fn1"></a>
I might potentially have a much better solution brewing a few weekends from now. I should finally have some free time to code a lot of tools to help speed up conversions/catch common mistakes I find in EPUBs. Hopefully I can code a Footnote Tool 2.0, which I can then release to the public after polishing.