Jasper Engine

Took the car to the shop today.. Diagnosis... spun rod bearing. Thank god its still under warranty. so i just took off all of my goodies to get it fixed
Anyways. what i cant take out is the intense pcm. I think what they are planning on doing is ordering a new motor from jasper and installing it,(it would be cheaper then rebuilding the whole engine again). What i was wondering is if they do that am I going to have to have the pcm reprogrammed again? Or am i just going to have to have the case learn done again??? Thanks