Ok, so LetsEncrypt is awesome but it has one MAJOR pitfall as of version
Ubuntu, there is no
delete option for the cli.
There is however a workaround that will allow you to remove the domain from the cert renewal process and the chain.
sudo rm -rf /etc/letsencrypt/live/[Domain] sudo rm -rf /etc/letsencrypt/archive/[Domain] sudo rm /etc/letsencrypt/renewal/[Domain].conf
I have found that you must also remove the virtual host configuration from the
/etc/sites-enabled directory as well as well as the sites webroot directory in
sudo a2dissite [Domain] sudo service apache2 reload sudo rm /etc/apache2/sites-available/[Domain] sudo rm /var/www/html/[Domain]
After completing these actions the domain will no longer attempt to renew with your cron job, and it will not show up in the ncurses menu when you run