Open the desktop version of EndNote and follow the instructions below to identify and remove duplicate records from your EndNote Library:

• With the library window open, click on the All References group to show all references.
• From the menu select Library > Find Duplicates. EndNote will display a Find Duplicates dialog, where you can compare duplicates and decide which version to keep and which to delete. 
• For each set of duplicates, you have the option to:
  • Keep This Reference to save that particular reference and throw the other one in the trash.
  • Skip to leave both references in the library, intact. They will appear in a temporary Duplicate References group, so you can review them later.
  • Cancel to automatically instruct EndNote to select the most recently-entered version(s) of each duplicate reference as the one(s) to be removed. Move the selected references to the Trash to remove them from the Library. (Moving all references in the Duplicate References group to the trash will remove all copies of all references duplicated, including the original. Ensure only selected references are moved.)

You can also automate the deduplication process using the Primary Reference tool. Select from sorting criteria of Oldest, Newest, and Most Complete then click Keep Remaining References. Selecting Oldest will remove the newest version of the reference, selecting Newest, removes the oldest versions and choosing Most Complete retains the reference with the most information.

Find out more about working with duplicates in your Library via Clarivate's FAQ: Steps to remove duplicates from your EndNote Library or watch the video from Clarivate below.