If your most current library is in EndNote Web, you simply need to create a new blank desktop library and sync it.
However, if your most current library is in the desktop version, then you will need to break the connection with
the Web version, and reset it.
1. In EndNote Web, delete all references, groups and empty the trash.
2. In EndNote desktop, add this to the end of your E-Mail Address in the Sync preferences: #!resetLocalSync
Note: This is case sensitive. So, if the email address was email@example.com, you would change this to firstname.lastname@example.org#!resetLocalSync
3. Click the sync button, you will be prompted to re-enter your EndNote Web email address, and to close and re-open EndNote.