I just added a second domain to my cert a little while ago, and did exactly that-- ran
nextcloud.enable-https lets-encrypt again, this time with both domains. That script restarts Apache, which picked up the new cert. Have you tried restarting Apache yourself?
$ sudo systemctl restart snap.nextcloud.apache.service
If that doesn’t work, and you’ve verified that the new certs are correct and the old certs aren’t around, I’m not sure what’s going on there, but we can take the nuclear option.
First of all, disable HTTPS (this just removes a symlink, it doesn’t remove any certs):
$ sudo nextcloud.disable-https
Then blow away any certs that are there (this includes self-signed certs, Let’s Encrypt certs, everything). Make sure you get this command right, you don’t want to delete anything else in the
$ sudo rm -rf /var/snap/nextcloud/current/certs
Then pretend you’re enabling HTTPS for the first time:
$ sudo nextcloud.enable-https lets-encrypt