Hello Adam,
You can do the following to remove the duplicates from your library.
You can then turn off the setting for Cite While You Write to remove duplicates in the Bibliography.
On Windows go to Edit then Preferences or on a Mac go to the EndNote menu then Preferences.
Click on Formatting on the new window.
Unchechk Merge duplicates in bibliography.
On Windows click OK, on a Mac click Save and then close the window.
You can then go back to Word and use Update Citations and Bibliography.
If you need additional assistance.
Please contact Technical Support directly
1-800-336-4474 option 4 then 1
or
We are here to help whenever you run into issues.