Hello, maybe someone will find this old thread in the future. I had the same “problem” with c9r files appearing in the root of “My Drive”, tried to recover them without success etc.
It seems to be a “feature” of Google Drive with shared files being deleted by another user. If you own a file and another user deletes it, the file will be deleted for the other user, but not for you as the owner. It will be moved to the root of your “My Drive”. Maybe for the owner to have a backup I don’t know.
If you open the Google Drive website and check the file history for the c9r files in the root you should see different timestamps. An older one for the creation and a newer one for the moving to your root titled “Automatic creation” or something like this.
So there should be no data loss as long as the other user deleted the files with your permission…