It is likely that endnote will pause on the inserted citation, bring up the best matches including the correct duplicate, and you will confirm the right one, and move on.
(Your other thread is here: http://community.thomsonreuters.com/t5/EndNote-How-To/help-merging-references-in-word-same-reference-different/m-p/135996#M25374. You can see all your posts by clicking on your name and seeing them listed.)