How would FFF know which chapter you want it on? And how would it put it in there? Especially in light of FFF only doing minimum processing of prior chapters on update to preserve user edits? IE, the adapter's getChapterTextNum() isn't called for preexisting chapters on update.
I really don't think this is something worth that much special handling.
If you have remove_authorfootnotes_on_update:true you could consider turning it back off to maybe get something vaguely similar:
Code:
## AO3 authorfootnotes and inspiredlinks end up in the 'last' chapter,
## but if updated, then there's a new 'last' chapter, leaving multiple
## copies. This option applies the 'skip_on_ffdl_update' class to
## those tags which means they will be removed during epub reading for
## update. This will only effect chapters added after turning the
## setting on.
## Result: Only the last chapter will have end notes.
## Side-effect: An 'Update Always' that doesn't add a new last
## chapter will also remove the end notes.
#remove_authorfootnotes_on_update:false