I know one of thier reasons for not making copies was his program was too big but I never understood why they couldn't copy it after they got the mobile emitter.
I would think that they didn't want to rely so heavily on the mobile emitter. They've said more than once that they weren't completely sure how it worked since it was so much more advanced than their technology. What if the power ran out on it, or it was damaged somehow. if he was only in the mobile emitter in that case he would be lost.