FewMiles. When computer systems are switched, CP will be changing to the AC system of RESIII. T2 and T1 will see it first.
As for what system AC will choose when their current contract is up is as yet undecided. That's too far away at this time to worry about. Right now, they both need to be working on the same system as they are currently not compatible. There will however be a link added for checkin at either carrier in the near future. Date is yet to be confirmed.