Cert warning from client until browser refresh

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I'll get clean up the vhost config and try that, in the mean time here's the output of apache2ctl -t -D DUMP_VHOSTS

VirtualHost configuration:
*:443                  is a NameVirtualHost
         default server aghsandbox.eli.org (/etc/apache2/sites-enabled/agh.sandbox-le-ssl.conf:2)
         port 443 namevhost aghsandbox.eli.org (/etc/apache2/sites-enabled/agh.sandbox-le-ssl.conf:2)
         port 443 namevhost cmmsandbox.eli.org (/etc/apache2/sites-enabled/cmmsandboxes-le-ssl.conf:2)
         port 443 namevhost cmmsandbox.elr.info (/etc/apache2/sites-enabled/cmmsandboxes-le-ssl.conf:25)
         port 443 namevhost www.eli.org (/etc/apache2/sites-enabled/eli.org.conf:26)
         port 443 namevhost eli.org (/etc/apache2/sites-enabled/eli.org.conf:44)
         port 443 namevhost elr.info (/etc/apache2/sites-enabled/elr.info-le-ssl.conf:2)
         port 443 namevhost www.elr.info (/etc/apache2/sites-enabled/elr.info-le-ssl.conf:12)
*:80                   is a NameVirtualHost
         default server lovins.eli.org (/etc/apache2/sites-enabled/000-aghdefault.conf:1)
         port 80 namevhost lovins.eli.org (/etc/apache2/sites-enabled/000-aghdefault.conf:1)
         port 80 namevhost aghsandbox.eli.org (/etc/apache2/sites-enabled/agh.sandbox.conf:1)
         port 80 namevhost cmmsandbox.eli.org (/etc/apache2/sites-enabled/cmmsandboxes.conf:1)
         port 80 namevhost cmmsandbox.elr.info (/etc/apache2/sites-enabled/cmmsandboxes.conf:17)
         port 80 namevhost www.eli.org (/etc/apache2/sites-enabled/eli.org.conf:1)
         port 80 namevhost eli.org (/etc/apache2/sites-enabled/eli.org.conf:17)
         port 80 namevhost www.elr.info (/etc/apache2/sites-enabled/elr.info.conf:1)
         port 80 namevhost elr.info (/etc/apache2/sites-enabled/elr.info.conf:17)
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