The sync may have been interrupted or disconnected as the number of references in EndNote desktop is fewer than EndNote Online.
- Create a new library by clicking on File > New
- Uncheck Save as package and save it under the Application folder which is the most stable location for MacOS
- Click on Library > Sync to sync the references from EndNote Online to EndNote desktop and wait for the syncing process to be completed.
Note, this is a solution for EndNote 20 users.