I'd bet nothing would happen to the CI program on the external processor. The internal processor may get the memory erased but I think all the internal processor does it process the signals the external processor gives. The heart is the external processor and is replaceable.
I'd say that the paddles are positive and negative. The electrical current travels from one paddel to the other thus making a complete circuit. There would really be no reason the electrical current would travel to the head unless someone put the electrical paddle on the head. If so, maybe it is no more current discharge than a normal electrical shock would be and I get shocked a lot getting off the couch and touching my child, wife, cat, dog, wall switch, etc and I can still hear fine.
I've also experienced what I thought was static electricity discharge through the coil when I was wearing my XM recorder/Ipod listening to it with a PA Cable with the device in my pocket of my jacket. Interesting feeling, nothing happened, could still hear fine, everything functioned the same. No problem.
I'm not the expert in the field and may have how this works totally misunderstood but like others have said, I'd rather have them use the shock paddles instead of leave me for dead.