Things just didn't disappear. But Bruce recalled an incident with River when he first arrived in the City, she had mentioned something he had never forgotten. Another version of himself had been there before. Completely different.
Bruce had forgotten about it until now.
"Well...use what ever you need to. If Tony's equipment can't find him, then nobody can." It was truth, Tony had the best equipment money could buy and brains could build. If Oswin couldn't find what she was looking for them maybe he had disappeared.