Not a theory, but something to maybe note:
A lot of people wonder why Kirkland killed Lennon without asking him who RJ was. I mean, Kirkland has tortured people for information in the past, why wouldn't he even ask? All he asked is "Do you recognize me?".
My guess:
It wasn't Bob asking Lennon, it was Micheal. Micheal was asking Lennon to check if his brother Bob was searching for him. Once he found out Lennon didn't know, he filled Red John's [possibly his own] orders to kill Lennon.
