I guess the first question is whether endnote temporary citation appear when you convert bibiography to unformatted citations. If so, you are fine.
Was the section where they “disappeared” formated with endnote to begin with or was it a co-author inserted chapter? - I am guessing that one of the co-authors used word to insert citations and not endnote, and when combined endnote tried to convert them? Not sure what happens in that case. Do you not have access to the pre-manipulated version?