Installed exactly like the tutorial. [QUOTE="That's not needed. Its the part which automatically modifies apache config files and that's exactly what should not happen as certbot duplicates existing config which then causes issues, so you don't need that package. It does not hurt when you installed it though unless you would actually use it.[/QUOTE] So we will not install it then.
Good news, it is working now. Thanks to all that helps. Here is what I have done: Code: mv /etc/letsencrypt letsencrypt_old mv /usr/local/bin/certbot-auto certbot-auto_old mv /opt/eff.org eff.org_old cd /usr/local/bin wget https://dl.eff.org/certbot-auto chmod a+x certbot-auto ./certbot-auto --install-only After that issuing the LE SSL was working for the one subdomain, but we lost access to the ISPconfig control panel as apache did not restart. Had to do the following. Code: cd /etc/apache2/sites-enabled/ unlink 100-domain.com.vhost You need to unlink all of the sites that you see there. We did a mistake that we deleted ispconfig vhost, in our opinion that should have been left there but run: Code: ispconfig_update.sh to re-issue a certificate to gain access to the panel. In any case, once we gained access to the control panel, we start issuing SSL and back to normal. Thanks to Till, Croydon and elmacus
