Once in a while subdomain are not longer existant or moved to a different server.
The solution to remove such domain and allow certificat rewal is as follow:
Either you have created your certificat with --allow-subset-of-names or you need to edit the renewal config file (eg: /etc/letsencrypt/renewal/example.com.conf) and ensure a key allow_subset_of_names = True in the [renewalparams] section.
Renew the certificat (it should succeed with an alert regarding the missing subdomain).
Once done, you can remove the subdomain line from the renewal config file.
A more officially recommended way to do this is to rerun your certificate request with certonly and with --cert-name specifying which certificate to act upon, as well as a -d list of all of the domains that you do want to be in the certificate. The benefit of this relative to --allow-subset-of-names is that it will fail with a useful warning if any of the other names in the certificate couldn’t be renewed. If you use --allow-subset-of-names, the renewal could potentially succeed with the loss of unexpected or unintended names from the certificate in addition to the specific name that you intended to remove.