After updating to the current version of cPanel every customer site on the server now displays a 404 error page can not be found. I re ran the update to the stable version now about half of the sites still show the 404 error, anybody have a suggestion on how to fix this?
You need to check for errors and problems in httpd.conf and check the apache error_log while visiting the pages. One common issue (which you'll see in an apache restart) is if you have a missing NameVirtualHost statement from httpd.conf for the shared IP address.