Hi Marko,
You have to create /etc/letsencrypt/live/FQDN not FQDN1.
The best way will be to recover it from a NethServer backup…
For the vhost, you do not have to create any new directory for the certificate in /etc/letsencrypt/live/, Let’s Encrypt will create it.
DEMAND OF THE FIRST CERTIFICATE
Here toto.com is the original FQDN 
GUI 9090: System → Certificate → Actions → Request Let’s Encrypt certificate
toto.com (for the default domain in /var/www/html/) 
Set it as the default.
CREATION OF THE VHOST
If the vhost is created with the GUI 9090, the vhost directory will be a number. (/var/lib/nethserver/vhost/1234567...890123)
If the vhost is created with the GUI 980, the vhost directory will be the name of the vhost (/var/lib/nethserver/vhost/titi)
DEMAND OF THE SECOND CERTIFICATE
titi.com (for the vhost in /var/lib/nethserver/titi)
Here directory titi.com is created by Let’s Encrypt
after the demand of the second certificate.
GUI 980: (to associate the second certificate to the vhost titi)
Management → Virtual hosts → General → end of line of titi → Edit → SSL/TLS certificate → choose /etc/letsencrypt/live/titi.com/cert.pem → SUBMIT.
If you go to https://www.toto.com, it will take the certificate of toto.com
If you go to https://www.titi.com, it will take the certificate of titi.com
Michel-André
P.S. You do not have to wait 7 days, you can try it now, as you already asked only one time for each certificate; there should be 4 demands left with the same set of domains.