There is some hidden stuff in fields, that if you do the updates in the right order, the fields get updated to your library. Tricky, but try reading this and see if it avoids the problem? http://endnote.com/kb/131973
As a last resort, I have unformated the original document, compared it to the unformated new document, and then accepted (or rejected changes to) my citations, and accepted the other updates. – then reformat with my library. I found that the safest way to recover the correct temporary citations with “record numbers” that otherwise may have been inadvertantly changed.