Thanks @DarkSteve It's good to know what is and is not available in the current release as it can save me time.
"In the meantime, is it possible to avoid renew errors by manually removing the unwanted domain from the renew conf file?"
Do you know how this would be done - would this be the missing feature to be able to remove domains - which isn't there yet?
In another thread, removal of the entire cert, to recreate it, doesn't appear to be straightforward, according to: