What Leanne says is possible, but I think there’s a likelier culprit: Are you using the Track Changes feature when you made your edits? EndNote and Track Changes do not play well together. It may also be a field code issue, and so you may find the procedure outlined in http://endnote.com/support/faqs/CWYW/faq15.asp helpful.
Remember, you can always get in touch with us if you hit a wall and you need “official” support.