When you login to WHM and all the IP’s are missing.

If you have 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.

Run the following to restore the IP addresses:

# /etc/rc.d/init.d/ipaliases restart

You may have to restart named to get DNS going again as well. Restart named again cause it cannot bind on the new IPs from ipaliases.

# service named restart

The issue of why is explained here:

https://forums.cpanel.net/threads/cpanel-loses-all-but-primary-ip-address.160393/