Guys, I just went through this this last week. My fans were running (I had already purchased the new relay to avoid a trip to the dealership but,,,)
Took the car in Monday morning. I parked it in a tech's service bay who was on vacation. I then un-married my Accessport (with a TDC base map) from the ECU. Due to the mods (TGV delete and all), I told them that the car could not be started with the stock ecu in place and that I would need to re-install my programming after the new ecu was installed. They agreed, allowed my car to stay inside and didn't do anything to it execpt to remove the old ecu and install the new one.
Took car in on Monday, They called me Wednesday at 1 PM to tell me that the new ecu was in and to come on in. I went in and reloaded the base map and the real time map (my dyno tuning) back into the ecu.
However, when I went to start the car, it wouldn't start. After a couple of minutes, the chief tech remembered that our cars have an anti-theft immobilizer and the keys have a transponder in them and need to be "reintroduced" (or something like that) to the new ecu. Bring all your keys with you because they have to do them all at the same time. He did the reintroduction and the car started right up.
Just make sure you follow the directions when unmarrying and loading into the new ecu.
Hope this helps.