I'm pretty sure they have his pokemon. But did they take his bag? Because it holds the egg he got earlier.
Edit: After rereading your post, I've discovered that they may not have needed to take his pokemon. He can't very well bust out of that room. Though I'm not quite sure, so until I know what all he has, I can't really post.
Diamond is lurking somewhere. I'll send him a VM to see if he'll do anything. How about you make a post of Israel and Yasumi moving the unconscious John out away from the pokemon center, and if he doesn't get back to us by then, John will be officially captured.Sound good to you?