This is typically due to having avahi improperly configured and running on your machine, it will withdraw the IPs on running either
a) a reboot, or b) a network restart, so you can check you logs at /var/log/messages for avahi.
You can either stop avahi or properly register your IPs in avahi for these to be recognized. That service is what is causing the issue to occur.
To restore the additional IPs and ensure they are listed in WHM as well as ssh again, run the command below:
# /etc/rc.d/init.d/ipaliases restart
You may have to restart named to get DNS going again as well. Restart named again because it cannot bind on the new IPs from ipaliases.
# service named restart