Just magic 
They (OneDrive) must have fixed the issue. IĀ“m using now the last Canary with the patched dll. It was taking about 5-6 hours to complete the daily backup and today it took only 55 minutes. IĀ“ve tested the list of files with the console application and there was no repeated entries.
Mine seems to have auto-magically fixed itself also 
Mine is also working correctly again. Great to see that.
A miracle. Mine is working again, too!