OP I have had this set up for quite a while before going the dark side with the SC. With having the Dinan XPipe and the stage 2 software you should get no CEL light. If you brought the car in for service they may have reflagged the vehicle and removed the software. Always make sure to tell them you have the Stage 2. I'm sure they know as you have probably told them and they did it, but people in the service can have repeated brain farts.
It should not cost you anything to get it reflashed.
Happy driving and be safe. Great sound with the Dinan XPipe