I have the same problem. I run the lateste version of endnote
Sync Details
Sync was last run: Sunday, July 30, 2017 at 13:22:13 PM +0100
Sync Status: There are changes that need to be sent.
Error Code: Server.invalidInput
Error Message: Server.invalidInput - This reference is already expunged
How do I solve this?
Thank you. TW