conflict with index brackets

You can change endnote to use any pair of unique characters as the temporary citation delimiters.  Square are more commonly used for other things, but might work in your case or try $@ as a pair? 

You can change the endnote preferences to use an alternate pair (see capture2 attached image) or you can try to edit the temporary citation delimiters from the bibliography setting in the document (see capture.jpg attached) but that might not work if it is crashing when you try to open the document.  Try turning off auto formatting on the endnote tab before it tries to update the citations.