A family of Microsoft word processing software products for creating web, email, and print documents.
If you've somehow managed to delete just the endnote reference without affecting the numbering of other endnotes, that suggests what you deleted was the reference in the endnote, not the reference in the document body. If not try running the macro at: http://www.msofficeforums.com/word-vba/16610-repair-two-interspersed-endnote-numbering-schemes.html#post47377
The macro there should repair the endnote structure, enabling you to delete the unwanted one.
If that doesn't work it's possible the document has acquired some form of corruption. Corrupt documents can often be 'repaired' by inserting a new, empty, paragraph at the very end, copying everything except that new paragraph to a new document based on the same template (headers & footers may need to be copied separately), closing the old document and saving the new one over it.