You need to specify all of the names, including those already registered.
I used the following command originally to register some certificates:
/opt/certbot/certbot-auto certonly --webroot --agree-tos -w /srv/www/letsencrypt/ \
--email me@example.com \
--expand -d example.com,www.example.com
… and just now I successfully used the following command to expand my registration to include a new subdomain as a SAN:
/opt/certbot/certbot-auto certonly --webroot --agree-tos -w /srv/www/letsencrypt/ \
--expand -d example.com,www.example.com,click.example.com
From the documentation:
–expand “If an existing cert covers some subset of the requested names, always expand and replace it with the additional names.”
Don’t forget to restart the server to load the new certificates if you are running nginx.