Yeah, I think you need to go to the computer at the Pokemon centers and withdraw him.
Before you take him out, make sure you have less than 6 that you're carrying too.
This should be on the iPhone forum!!
Damnit you are right. It should be on the iPhone forum.
And btw -- I did go to the Pokecenter and try to get him from the computer. Though on the pokedex it has a ball icon indicating he has been caught, he is nowhere to be found in the computer. Very confusing.