Word is not a simple program to use if you are trying to do something complex, as you are. I think it is the most powerful word processing program on the market today. It is not a typewriter, nor is it any other program. You need to learn how to use your tools! Here, your problem started with someone not knowing Word messing with your endnotes.
I am an old curmudgeon and unapologetic about it. When I had to do endnotes in school, it consisted of putting it on index cards and typing them in at the end of my writing, rolling the paper down a bit to do superscript in both the body and the endnotes.