It's definitely the filename encryption/obfuscation that's triggering the problem because it makes the filenames look like gibberish, and Microsoft are using that as an indicator.
I have a family O365 account, so 6*1TB of storage. Two of them I use for backups:
% rclone about OneDriveBackups:
Total: 1.005T
Used: 753.709G
Free: 275.291G
Trashed: 731.979G
% rclone about OneDriveBackups2:
Total: 1.005T
Used: 720.914G
Free: 308.086G
Trashed: 244.630GDrive 1 does not have filename encryption, so everything just gets the ".bin" extension and doesn't trigger the alert. Drive 2 has a combination of no-encryption and obfuscation and it does trigger the alert; I just logged into the web site and it popped up the nasty message;
I hadn't noticed 'cos rclone was still working nicely without error 