Hi,
had the same on a Mac Desktop Client (newest V). After 3-5 attempts per Notebook (Both around 5k notes), with failed status, EN finally saved my notes as multiple html. Annoying as hell and I hope there will be an update for the backup 'feature' soon.
To me it seems, that EN is loading Notes in the Background and can't do it for a huge number until the backup process stopped. Hence after a couple of attempts every note has been downloaded fresh and it works. But ... thats just a guess.
Tom