2001 Ford Focus Check Engine Light

I recently picked up my vehicle after having a new engine installed in the car, I drove 2 miles down the road the check engine light came on, I drove back to the repair shop the mechanic told me an old code was the problem, so he reset the light, thought things was fixed then 7 miles down th road the light came back on again, the car seems to be running fine, but I just don't understand if it is an old code prior to the old engine then why is the computer still picking it up. Just trying to understand. The mechanic told me to drive for a couple days see if it goes off, then to come back in if it doesnt. Could you explain why an old code may still be stuck in the computer.