I ran into and issue that took far to long to resolve. I wanted to do some .htaccess file redirects with pdf files. I needed to change the config for a particular nginx vhost to allow apache to handle pdf files and not nxginx. Finally I found ejsolutions’s post on nginxcp.com/forums. The basics are you create your own vhost files for a particular cPanel account and then copy them over top whenever the rebuildvhosts script is run.