Just magic 
They (OneDrive) must have fixed the issue. I´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. I´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!