[AlanHK]

You really need to give some examples of the links in the text and the corresponding footnotes.

Anyway, likely the original links to notes at the end of the chapter were something like:

^{<a href="../Text/#ftn_fn2" id="ref_ftn_fn2">2</a>}

this points to the link with id="ftn_fn2" in the same chapter.

If you have moved all the notes to another file, footnotes.xhtml, you need to change the links to:

^{<a href="../Text/footnotes.xhtml#ftn_fn2" id="ref_ftn_fn2">2</a>}


You can do that by S&R. Change:
Text/#
to
Text/footnotes.xhtml#
As always, save before doing anything, do one and see if it works before doing them all.

Make sure the ids don't duplicate in each chapter (e.g., starting "ref_ftn_fn1" in each chapter, and the notes ids are also unique). Otherwise chapter 2 note refs will go to chapter 1 notes.
Then you have to add text to each to make them unique.

You seem to be lucky if the links from the notes back to the text work, these must already have that filename in the link.
That is more tedious to fix as there are more than one text file.