Hi,
These notifications should normally only come when a lot of files/folders have been deleted (in large quantities).
During the encryption process, we create a new version of each encrypted file or folder and keep all data until we make sure we have encrypted all files and folders 1: 1, and delete the old files and folders after verification.
This applies to all cloud providers, not just OneDrive. This is the only way we can encrypt data and save the changes in the cloud.