$ sudo certbot delete --cert-name <domain/subdomain>
ex :
$ sudo certbot delete --cert-name cert.agink.id Saving debug log to /var/log/letsencrypt/letsencrypt.log - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Deleted all files relating to certificate cert.agink.id. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -