So you will have a main file which would be
This could have a default server in it, Im not sure.
Then in the sites available there will possibly be a file called default. But inside the nginx.conf it only includes the symlink folder which will be /etc/nginx/sites-enabled/*
So if you have removed the symlink for the default then it wont get included.
See the config page here on how to set it up the default (second code block on that page)