In EndNote Desktop, sync, or resync, your EndNote Desktop and EndNote Online libraries by click on the Sync button in the EndNote toolbar:
Setting EndNote Desktop and EndNote Online to automatically sync to each other
You can set your EndNote and EndNote Web libraries to sync (merge) automatically in the background while you work. Setting your preferences to enable syncing will cause your libraries to sync about every 15 minutes.
Click on Edit/Preferences:
1) Click on Sync, and then 2) on the Enable Sync button:
To create an EndNote Web account, click on Sign Up. If you already have an account, fill in the e-mail address and password for your account, and click on OK.
This will return you to the original form. Your e-mail address and passwords will be filled in automatically. The path to your open library should be displayed in the Sync this EndNote Library box. Check Sync Automatically, and then click on OK: