DocumentRoot for every site changed?

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http://forums.cpanel.net – I ran the IP migration manager, ran an update on cPanel (currently at WHM 11.38.1 (build 13)) and then ran EasyApache on a basic build with no front page, and IonCube, mod_security, and GD enabled. Then when I visit any website I'm hosting, I get prompted with the lovely WHM default website page. I looked into my httpd.conf file and found the issue: somehow, the DocumentRoot for every single virtual host had been changed to "/usr/local/apache/htdocs". It SHOULD be /home/%username%. Any idea on why this switched and how to fix it without manually updating a thousand entries? (HowTos)