First of all, add an entry to the DNS zone; you can do this in your host panel.
Pointer records = A
Target = IP of the server
Remove existing one with this command:
sudo rm -rf /etc/letsencrypt/live/example.com
sudo rm /etc/letsencrypt/renewal/example.com.conf
sudo rm -rf /etc/letsencrypt/archive/example.com
Stop server:
sudo service nginx stop
Create a new one certificate:
cd /opt/letsencrypt
./letsencrypt-auto certonly --standalone
Then add all domaines there separated by comma;
example.com www.example.com subdomain1.example.com sub2.example.com
Restart server:
sudo service nginx restart
Update nginx sites
sudo rm /etc/nginx/sites-enabled/example.com
sudo ln -s /etc/nginx/sites-available/example.com /etc/nginx/sites-enabled/