Zod enter his own Command Key and terminate Jor-El's A.I. But, he did not terminate the A.I of Jor-El's programming. If you remember, when Superman it's with Louis trapped on the Spaceship before Zob orders the Terraforming of Earth, Jo-El uploaded himself to that Ship with out even using the Command Key. He helped designed the Ship. With that said: That also means that his main Source Code could regenerate and upload it self anywhere. Zod ask the Ship: Have you completed OVERRIDING Jor-El's program? The ship answered: Override Complete. There for, if Jor-El was the father of the technology that allow him to upload his Sub-consciences and memory through eons and galaxy's.. Should we also assume that he knew how to back up him self as Source Code?