I don't know if anyone else has had this problem, or if I'm branding myself as an idiot by having it. Be this the case, than those like me can benefit, while the rest of you can scoff at me, and rightfully so.
In shortening a chain yesterday, I pushed a pin completely past the plate. I thought I was ruined, except my genius girlfriend though of using a bobby pin to hold the chain pin between the chain tool driver and the plates so that it could be driven back through.
Two pins, one chain, a happy bike.