What output style is being used in the document (not in the Endnote program)? I suspect that it is the wrong one? What do the unformated termporary citations (in curly brackets?) look like?
Finally, if the fields have been corrupted, I suggest unformating the citations that you can in the pre-edited version and in the updated version. Do a compare and then move thru the merged document and accept reject the appropriate elements that differ. Next time, I suggest that you only share an unformatted version with non-endnote colleagues to avoid corruption. The content in those fields are “enormous”!