I try to explain:
In notes, href="file1(or as you like).xhtml#ftn1a" id="ftn1b"
In the other files, href="notes(or as you like).xhtml#ftn1b" id="ftn1a"
Merge all files into one (file1)
Split file1 accordingly.
The editor is responsible for doing all the work.
Good luck! (and first make a backup)