Certbot uses the list of subject names in the most recent certificate as the list of subject names for a renewal:
Normally if you want to change this list you should force a renewal with a new list of subject names, like
certbot --cert-name example.com -d one.example.com -d two.example.com -d three.example.com -d example.com -d www.example.com --force-renewal
If this succeeds, then you have an new certificate that covers exactly those names rather than whatever names were covered before.
I believe that this is currently the only way to do it because I believe the domains setting is explicitly ignored in the configuration file, due to a common mistake where people were putting this setting in their cli.ini files.