I have a question about Certbot. I went through the letsencrypt.log file, and I can see that it still tries to renew certs for 2 old domains, which I don’t have anymore on the server.
Is there a way to delete them out in some way?
If those deleted domains were setup using Virtualmin at the first place, and later manually deleted (rather than using Virtualmin), then the issue you’re experiencing could happen.
It can be fixed by looking to Virtualmin domains configuration directory located at /etc/webmin/virtual-server/domains, and finding configuration files related to old domains.