The OP says that all notes are in the same file as where the footnote reference exists and that all the references take him back to the cover.
I'm betting that doing a replacement of all instances of
Code:
href=../Text/index_split_000.xhtml#anchor
with
would solve the problem as you only need the anchor reference and not the filename if it is in the current file.
Just make sure you have a backup before performing a "replace all".
BobC