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?
Hello 
You can try rebuilding the Apache configuration file via:
Check the cPanel userdata files if the issue continues. EX:
Are the document roots accurate in these files?
Thank you.
You can try rebuilding the Apache configuration file via:
Code:
# /scripts/rebuildhttpdconf
Code:
/var/cpanel/userdata/username/domain.comThank you.
I think you should try to rebuild httpd conf file as I think this will fix your issue, also just FYI if made any changes in httpd.conf manually then do not forget to update the distiller entries.