This is not as bad as it sounds. I’ve summarized the OneDrive behaviour here: https://www.reddit.com/r/Cryptomator/comments/fhw78k/microsoft_onedrive_detects_cryptomatorencrypted/
When you dismiss checking your (encrypted) files, they will be removed after 30 days!
This is flat out wrong! Nothing will be deleted.
What Microsoft does is warn you. Nothing more. They *think * that your files have been encrypted and that you lost access. They remind you as a courtesy about their 30 days backup, from which you can restore the files. That’s it. They are just trying to be helpful. Read the screenshots in my reddit post from march.
Note the very last paragraph:
Update 2020-03-18
You can not turn the warnings off. But you can choose to ignore the warnings and mails. After the third mail Microsoft gives up and sends you a „Last Warning“ mail and the shuts up. After that you can even use the GUI without being prompted.