I'm running Debian 9.2 with nginx and let's encrypt on a single droplet. I have got SSL to work on fine after following the tutorial for one domain with this default setup in sites-available:

server {
        listen 80;
        server_name primarydomain.com www.primarydomain.com;
        return 301 https://$server_name$request_uri;
}
server {
        # SSL configuration
        listen 443 ssl;

        server_name .primarydomain.com;

        root /usr/share/nginx/html/primarydomain.com;

        include /etc/nginx/sites-available/include;

        include snippets/ssl-primarydomain.com.conf;
        include snippets/ssl-params.conf;
}

But then I wanted to have another domain as well as subdomain connected to the same droplet but another /usr/share/nginx/html/ folder so I set it up like this:

#Primary
server {
        listen 80;
        server_name primarydomain.com www.primarydomain.com;
        return 301 https://$server_name$request_uri;
}
server {
        # SSL configuration
        listen 443 ssl;

        server_name .primarydomain.com www.primarydomain.com;

        root /usr/share/nginx/html/primarydomain.com;

        include /etc/nginx/sites-available/include;

        include snippets/ssl-primarydomain.com.conf;
        include snippets/ssl-params.conf;
}

#Test.Primary
server {
        listen 80;
        server_name test.primarydomain.com www.test.primarydomain.com;
        return 301 https://$server_name$request_uri;
}
server {
        # SSL configuration
        listen 443 ssl;

        server_name test.primarydomain.com www.test.primarydomain.com;

        root /usr/share/nginx/html/test.primarydomain.com;

        include /etc/nginx/sites-available/include;

        include snippets/ssl-primarydomain.com.conf;
        include snippets/ssl-params.conf;
}

#Secondary
server {
        listen 80;
        server_name secondarydomain.com www.secondarydomain.com;
        return 301 https://$server_name$request_uri;
}
server {
        # SSL configuration
        listen 443 ssl;

        server_name .secondarydomain.com www.secondarydomain.com;

        root /usr/share/nginx/html/secondarydomain.com;

        include /etc/nginx/sites-available/include;

        include snippets/ssl-primarydomain.com.conf;
        include snippets/ssl-params.conf;
}

Unfortunately this did not work out at all as I thought it would. Is it something with let's encrypt I need to configure that I've missed perhaps?