# To update domains and certificates on remote server you should download your letsencrypt configuration directory and run the following command
sudo certbot certonly -d beta.example.com,www.example.com,example.com --manual --preferred-challenges dns
or
sudo certbot certonly --cert-name example.com-0001 --expand -d beta.example.com,www.example.com,example.com --manual --preferred-challenges dns