PCM and tuner problem

So a week ago my ac stopped cooling, it works, except it gives out hot air only. I took my car to the dealer (I have an extended warranty) and they had diagnosed it was the cooling fan, so I went back a couple days later when the piece was in. After waiting about 2 hours. They told me that they would need me to come in again, and said they installed the fan but my PCM isn't working and they couldn't get it to reset and get the fan working. So they're ordering a new PCM for my car... My problem is will the new PCM be considered to be a different car by my SCT tuner?

Also I kind of doubt it's my PCM... I'm not getting any error codes or check engine, and wouldn't something like the PCM being faulty cause some more serious problems? The other thing is my tuner has been working just fine on my car, and I had returned it back to stock right before going into the dealer. Any insight on this would be great...