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This error happens with EndNote sync, and your EndNote online account not being able to update references. This is mostly caused by a corrupt PDF attachment in your library.
This should have two potential solutions, depending on the problem itself.
If you know which PDF is actually causing the issue, you can try to manually remove it from your EndNote library.
If you are not certain where the corruption is coming from, you can create a new blank library (EndNote: File > New), and save it in a good safe location. Do not save it in a folder synced by other sync services like DropBox, OneDrive, GoogleDrive, iCloud, etc. On Mac this means that you should NOT save your EndNote library in the Document or Dekstop folders. We recommend the Home folder on Macs).
Then syncronize your new, empty library with your EndNote online account/library (EndNote: Tools > Sync), to recreate your library.
Should the issue be data that the Online service believes is deleted, and cannot properly synchronize, a new blank library will often be the simplest solution, instead of pulling apart the library trying to find the issue.