I installed webmin on my server not too long ago and I proxied it under webmin.domain.com. After a while, domain.com expired and I didn't renew it. When that happened, I used rm -rf to delete it (which wasn't a good idea) and now I can't remove it with certbot delete.
@JuergenAuer I think OP removed some files from a location not being /etc/letsencrypt/ with certbot now complaining about some files not being there for some reason. While I agree with the advice about backups, I believe it might be possible to fix the certbot issue regardless of a backup.
However, @andymatax doesn't give us much to work with. It would be very helpful to see the used certbot command and the output of it.