In season 5 Bob asked gale if they could trust Lisbon. So, somehow Lisbon was being used.
Did you realize that Bob told Lisbon about the "secret" photo of lorelei's sister? well I guess that photo was created by bob. He didn't eve brother about Lisbon taking the photo after the phonecall, was really weired.
I guess he knew Jane would contact Lisbon and somehow introduce the Roy history in Jane and Lorelei relation. So Bob expect:
-Lorelei would then run to find RJ and Bob would be following her, because he is hunting him.
-Lorelei would kill the man who gave her sister to RJ, since she didn't, Bob did in the hospital.
One thing comes clear to me, if Bob was RJ would him give to lisbon a photo with his nickname ROY? Don't think so.