My understanding is that this is being worked on and the ability to remove a domain from your cert will be included in a future version of the client. The client currently allows you to add a domain to a certificate but doesn’t allow you to remove one.
In the meantime, is it possible to avoid renew errors by manually removing the unwanted domain from the renew conf file?
The only other option I can think of is to simply delete the cert you have (along with it’s archive, renew config, and symlinks) and recreate it without the unwanted domain. It’s not elegant, and the new cert will count against your weekly limit, but the unused domain will be gone for good.