Hi there,
I had this problem as well. Did you change the file path of your EndNote library?
My syncing issues started after I renamed the folder where I keep my library. When I saw the file paths in the Sync preference weren’t matching the new file path I created, I renamed the folder back to its previous label. For some reason, I couldn’t change the file path in the Sync preferences menu in EndNote (EndNote team, can you address this, please??).
Once I reverted the library’s file path to its original name when I first started syncing the library, and restarted Endnote, the sync worked again.
I hope this helps. Took me a bit to figure it out.