Two ways. Delete one and replace it with the other in the document, is the simplest, but you should make sure your preferences (edit>preferences> formatting) are correctly set to do this (which they usually are by default). Of course, if the two references are duplicate in all the settings below, it may not know they are the same.
(Then I would delete the duplicate from your library. )
If you miss one, however, then it may still happen, in which case, I delete the duplicate entry in the library, unformat and reformat the paper, the duplicate entry you deleted will not get endnote to ask you where it is, and you can replace them with the other version. You must remember to reengage CWYW from the third tab when you reformat the bibliography.
Help in Endnote (this is from X3) elaborates:
Merge Duplicates in Bibliography
When this option is selected, EndNote automatically omits duplicate references from a bibliography. It is a good idea to use this option if you are citing references from multiple EndNote libraries in one paper. In this situation, the same journal article reference might appear in two libraries and would have two different record numbers. EndNote will not identify the records as duplicates unless you have this option set to merge duplicates.
When this option is selected, EndNote checks the bibliography for duplicate references during the formatting process. If duplicates are found, they are removed. References are considered duplicates if they are the same reference type (such as Journal Article or Book) and the following fields are identical: Author, Year, Title, Secondary Title (Journal, Newspaper, Magazine, Book Title, Series Title, Conference Name, etc.), Volume, Issue, and Pages.
Note: The Duplicates preference settings do not apply to this feature. The criteria for determining duplicates is fixed for the “Merge Duplicates in Bibliography” setting.