I have had Certbot/LetsEncrypt set up on my websites to ensure they use SSL. Lots of it works automatically but it seemed some of the autorenewal of certifications had some issues. Particularly, I had a domain that wasn’t active anymore as part of a certificate with a lot of domains. Here were a few handy links and commands for reference for managing certificates with certbot.
Certbot guide https://certbot.eff.org/docs/using.html
Certbot reference with apache https://www.digitalocean.com/community/tutorials/how-to-secure-apache-with-let-s-encrypt-on-ubuntu-18-04
Create a new certificate for a domain
sudo certbot --apache -d jeremykeeshin.com -d www.jeremykeeshin.com
This helps create a certificate for a domain.
Modify a certificate to only have a certain list of domains
certbot certonly --cert-name flipsideconvention.com -d flipsideconvention.com -d www.flipsideconvention.com
I had a certificate that had a long list of domains, this sets the certificate to just apply to these domains.
Delete a certificate
sudo certbot delete
After running this command you can type in the index of the certificate to delete.