Question about changing out my Trans Am's computer

[Lee9710]

Before I bought my 97 T/A, the guy that had it said he was driving it and it just shut down completely one day. It was then determined that the computer in the car was bad it it needed a new one. They ordered one from the local Pontiac dealership here and put it in. The guy that put it in then told the old owner that if he wanted his keyless entry remote to work again, he would need to get it reprogrammed. Now the service engine soon light stays on but doesn't give any recognizable codes. Since it is not the same computer it was built with, do I need to get it re flashed or should it have been fine when it was put in? Hellllllppppppp!