I wondered about a Onedrive glitch, but it would have had to been a long glitch 'cos it did it over 6 different rclone runs, referencing 5 different crypt remotes which are on 3 different OneDrive accounts and the whole thing took 14 hours to complete... and coincidentally happened the first run after I updated 
I also wondered if Microsoft had rolled out some change which caused rclone to think things needed re-uploading, but that would likely have impacted other people.
Ah well. Just an oddity!