Is your endnote numbering created using an automatic InDesign numbered
list, or are the numbers regular text?
Also, is this problem reflected also in the endnote references in the
main text, or only the endnote text at the end of the document?
If the problem is everywhere, you may want to consider going back to
Word, converting the endnotes to footnotes, and importing into InDesign.
Then you can get the numbering to restart with each section, and then
use a script to convert the footnotes to endnotes at the end of each
section (I think there's a free one floating around for that).
Perhaps there's a simpler way of doing it -- I'm not so familiar with
Word endnote import.