I had a number of domains all running on one host when I first set them up with certbot. One started to be serious, so I moved it to another host and ran certbot there. That all worked perfectly, but of course, the old domain is still part of the original certificate, so when I went to renew it, it came up with some errors.
Here’s a few commands that are going to help navigate this situation if you’ve found yourself in the same spot:
sudo certbot certificates
There’s no way to delete a domain from a certificate, the process is to renew it, but just for the domains you want to keep. Certbot will notice you’ve missed some and warn you that you’re effectively deleting them.
sudo certbot --cert-name <certifcate-name> -d <domain1> -d <domain-2>