I came across the same issue today, but fortunately found a quick solution (which might have been particular to my circumstances).
I recently migrated from 2013 MacBook Air to 2018 MacBook Pro, both using fully up-to-date software. iCloud Desktop + Documents was enabled on both machines. I successfully opened my EndNote X8 library on MBP. Later, while Apple Support helped me with an unrelated matter, I disabled iCloud and re-enabled it. When I opened EndNote today, I got the dreaded error message other users have mentioned. Not wanting to go through the labourious steps mentioned above, I checked my EndNote folders and found that many of them were in the cloud, but not locally downloaded (they had the cloud with down arrow logo next to them). I clicked on the cloud icon to manually download EndNote folders, then rebooted (because why not). On reboot, I was able to open my old library without having to go through the recovery process.
Just thought I’d offer this in case it helps anyone else!