Hi Mat,
There are significant differences in the architecture of the two boards, the Pi 2 version 1.2 board in many ways reflecting developments incorporated in the later Raspberry Pi3 - which PilotAware has not yet been adapted to run on. New PilotAware software issued on 23rd February has however been specifically designed to allow PilotAware to run on either version of the Pi 2 board.
There are two other issues to consider: -
Firstly, all software released since May 2016, which you need in order to get bearingless targets and audio alerts, is designed to work ONLY on units which have a PilotAware RF transceiver Bridge board fitted. if you aren't currently running a Bridge, you need to factor the cost of a Bridge and associated antenna into your calculations.
Secondly, the PilotAware licence is linked to the MAC address of your existing computer board. If changing to a new motherboard, you would need a new licence - which comes with the Bridge board - (though if you already have a Bridge, Lee can transfer your existing licence to your new setup).
Regards
Peter