I found the easiest way update certificates with certbot (on my server) is to temporarily stop apache / nginx and to run the following command. Once you have the congratulations line, you can restart your web services.
Updating SSL Certificates with ‘certbot’
sudo systemctl stop nginx
sudo certbot certonly --standalone --email [EMAIL-ADDRESS] -d thebytes.net,www.thebytes.net,[ALL OTHER SUBDOMAINS]