This thread seems a little dead but I just wanted to chime in incase anyone sees this in the future that hasn't done the update yet.
I have a stage 2 catless 2012 wrx. I brought it to the dealer to get the update done with an oil change. I unmarried the accessport before going inside the service dept. I handed them the keys and when the car was ready, I installed the accessport once again before leaving the lot and everything ran smoothly as it should. I dont think anyone who does this will have a problem either since I think the accessport maps will overwrite anything the dealer has done. The only plus/reason to doing this is that you had the latest stock ecm image backed up to the accessport (at least that's how I think it goes).