Allrght, I did a vulnerability scan on the web server, there was something about the version of nginx installed had a flaw in it, so I went ahead and patched the nginx install. Ofcourse only because it is patch thursday and it might as well be on a list of things todo. Well, everything went smoothly; I upgraded to the latest version, refreshed the website in the browser, checked my config file, and were good to go. I then promptly left for lunch and didnt get the chance to check back at the website until approximately 7 UTC. Well, the website was infact not good. it was down, and probably down since i made those changes. I began to search for the issue. A quick grep, showed that my config files all existed and contained the domain name and hostname of the website. So whats the issue, why is it not reading my configs? Well that was the problem, and quickly came the solution. When you upgrade the nginx installation it overwrites your previous config file. Im not sure if there was any other magick stuff I was doing in the config file before I updated, but I included the sites-available directory, and were good to go. So yeah, the site was down for aproximately 3 hours. Thanks chaps :)