There are two tools you can use to reboot your server from within WHM.
They have their own category, called System Reboot.
1) Let’s go to Graceful Server Reboot first.
This tool is the preferred way to reboot your system. You should use this method whenever possible; it allows the server to close any processes your users may be running before restarting, storing data as it does so. This reboot method should not result in data loss.
2) To reboot, simply press Proceed.
3) Next, Forceful Server Reboot.
A Forceful Reboot will shut down the computer regardless of what’s running. It can cause data loss. You should avoid using this method whenever possible; only use it in the event the Graceful Reboot function is not working.
This method is generally preferrable to physically rebooting the server with the power switch, however.