Breaking the threads between sections won't help you, since the endnotes
and the endnote references in the text are completely static, regular
text. (However, if this is a long document, breaking the thread between
sections/chapters can significantly speed up InDesign, and it's one of
the first things I do when working on long docs.)
Now, presumably your endnotes references in the text have a character
style applied to them? Likewise, hopefully your endnote references at
the beginning of each endnote also have a character style applied to
them? If not, the first thing to do is apply a char style to these (make
2 styles -- one for the refs in text, the other for the numbers at start
of endnotes).
Next, is to find a script that can do maths based on a character style.
Must be one around somewhere... ... yup, here
you go:
http://indesignsecrets.com/free-script-to-change-all-numbers-in-a-document-using-math.php
So, now you just need to run the script, figure out how much to subtract
from each character style for each section so that the first note is 1,
and Bob's your uncle.
