There is no documented procedure to reboot the Cisco CallManager servers in the cluster. Reboot one server at a time, with the Publisher rebooted first. Once it is back up and the phones are rehomed on the new server, reboot the other consecutive Subscriber servers.
The recommended procedure is to first reboot the publisher before rebooting the subscriber (assuming your phones are registered to the sub.) That way you can make sure that the publisher completely recovers before you take down the phones by rebooting the subscriber.