It's been a year since I started using SSL certificate from Let's Encrypt and it's really easy to setup. I am using ubuntu on a Digital Ocean droplet and followed their simple tutorial to setup SSL for Nginx using Certbot.

I had a main domain and couple of subdomain and during setup when it prompt for domain selection I selected all of them. It did the job but with a twist, all the certification information were saved in single configuration file. Which was fine for a while until I deleted a subdomain.

Now after a year when I tried to update SSL I was getting error because of that deleted domain, it's certification information was still in that single configuration file. And according to this thread it's known limitation of Certbot that it's not possible to remove a domain from the certification file.

So here's how I solved the issue for my case:

Step 1 - Always make a backup just in case

sudo cp -r /etc/letsencrypt /etc/_letsencrypt

Step 2 - Remove the old certificate information from these locations

sudo rm -r /etc/letsencrypt/archive/<domain.tld>
sudo rm -r /etc/letsencrypt/live/<domain.tld>
sudo rm /etc/letsencrypt/renewal/<domain.tld.conf>
Replace domain.tld with your configuration file name

Step 3 - Remove all the certification references from Nginx conf
When you added the SSL Certbot adds the following lines in Nginx conf file which needs to be removed as well.

listen 443 ssl; # managed by Certbot
ssl_certificate /etc/letsencrypt/live/domain.tld/fullchain.pem; # managed by Certbot
ssl_certificate_key /etc/letsencrypt/live/domain.tld/privkey.pem;# managed by Certbot
include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot

if ($scheme != "https") {
  return 301 https://$host$request_uri;
} # managed by Certbot

Step 4 - Generate a new certificate
Finally I was ready to add new certificate but this time I didn't made the same mistake. This time I added certificate separately for each domain and subdomain.

sudo certbot --nginx -d
sudo certbot --nginx -d
sudo certbot --nginx -d
# etc ...

Step 5 - Reload Nginx
One last step was to reload the nginx server.

sudo service nginx reload

This worked for me and I am pretty sure I can updated each domain and subdomain separately from now on.