There is no migration procedure to move phones from Cisco CallManager Express to Cisco CallManager. Configure the phones in Cisco CallManager and point the TFTP server address of the phone to the publisher server in order to register to the Cisco CallManager. If the phones use DHCP, then you need to change the option 150 value on the DHCP server.
If there is an intention to completely remove Cisco CallManager Express, then it is possibly necessary to remove any route patterns that point to the Cisco CallManager Express. Also add the users to the voicemail system that the Cisco CallManager cluster uses and remove them from Cisco Unity Express.