Well because nothing can work as simple as uploading files my ftp decided it was only going to upload files at random and thus did not put critical files on the server when I updated as a result the entire thing is locked and the files are irremovable even though the server is off because the ftp tanked. The entire box will now need to be restarted so that the files will work. It is impossible to say how long this will take to fix.

I love how I upload stuff this way all the time and NEVER have problems until it is some big thing like this that breaks the entire fucking server.