DISCLAIMER: This method worked for me. I am not responsible for any damage caused if you follow these instructions! Read the documentation, learn what the commands do and then decide when or if you want to use it.
To remove a domain from a letsencrypt certificate when renewing, use the following command:
# certbot renew --allow-subset-of-names --dry-run
Remove the --dry-run if you are certain that this command does what you want.
And don't forget to reload your nginx/webserver/whatever.
A word of warning: The above command will remove a domain from the certificate if the challenge fails for whatever reason. Do not blindly use it! When using this command, read the output of certbot and make sure that only the domains get removed that you want to be removed.