For whatever reason, all servers that have the latest updates started
rebuilding the HTTPD.CONF file nightly and leaving out the /whm
and /cpanel aliases. It is really quite annoying!
I have confirmed this same problem against all of our own servers
and also the servers of several other hosts and in every case
those who updated within the past week had this same problem
with the /whm and /cpanel aliases vanishing from HTTPD.CONF
You can add the aliases back to the file and restart apache but
it will only be good until Cpanel rebuilds the file again.