You’re using an old version of Certbot (probably Ubuntu’s letsencrypt package, version 0.4.1) to renew certificates created by a new version of Certbot (probably certbot-auto installed somewhere). As you can see, old versions are unable to handle aspects of the renewal configuration files generated by newer versions of Certbot.
(The certificates aren’t different or incompatible, but Certbot’s configuration files are.)
You should find the newer version of Certbot you had installed and use it.
Alternately, you can wipe out /etc/letsencrypt – or at least parts of it – and start over with your older version.
(Alternately, you can compare and surgically edit the configuration files, but that’s not really worth the effort.)
As mentioned my @mnordhoff you are probably using a repo version of letsencrypt.
Please also note that letsencrypt has been deprecated and is now replaced with certbot being the official client for Let’s Encrypt certificates. This seems to be an eternal source of confusion and I wish the mods would sticky a big note about this.
You can simply eave your existing letsencrypt install in place and clone a new one from the repo and run all your commands as cert or certbot-auto and not letsencrypt or letsencrypt-auto from the /opt/certbot directory …