Before we continue, please update your theme first. You have updated your cornerstone but not the theme, it's causing incompatibility.
And it seems to be a URL rewrite issue and it's not supported by your hosting environment. Try accessing a non-existing page, instead of displaying Wordpress 404, it will then display the 404 error page built-in to hosting. I recommend contacting your hosting provider to correct or enable URL rewrite for Wordpress. That could be the reason why your permalink has