I got the impression that he knew all along. He buried Bob, and only came back for him after his time with Eb had concluded. My guess is that Bob told him that much in the time between DuMorne's death and the Council showing up.
That's
possible, but there's nothing in the text to support it, and the 'feel' of the conversation with Luccio goes the other way. Bob was always worried about
Mab getting her hands on him, in the conversations with Harry, not the Wardens.
We don't know the details of how they met, JB has said Harry became Bob's master at 16, which is part of why Bob is as lecherous as he is, imprinting on a teenaged boy as his new master. But how much Justin ever told him about Bob, or just what, we don't know, and I don't know if even
Bob knows about the Council termination order. It might well be part of the data he locked away when he no longer worked for Kemmler.
If Bob did know, at the very least I'd have expected some kind of comment from him on the subject when Harry arrived at Karrin's house in
Dead Beat wearing a Warden cloak.