Will Harry get back Bob so he can stop being super dork Bob?
I don't think so. I think Butters will keep Bob for at least several books. I mean just look what he did with Bob's help in only a few days of consultation and cobbling together of stuff. Before Ghost Story, Butters didn't have a lot to bring to the table in support of Dresden and the others. He had medical training to patch up holes, and investigative knowledge regarding causes of death. That was it really. Well, that and a pair titanium cajones when he needed to. (SUE!!) But really, the Hole Patching job is usually an after-the-fight kind of thing, and the medical knowledge was usually an Act 1 reveal kind of thing. After that though, Butters would usually fade back into the background.
With Bob though, he is participating directly. He is taking his brain (considerable) and applying it to this new area of reality, and coming up with spectacular things in no time. He has become the Magical Q to Harry's James Bond.
And really Harry didn't use Bob much in the later books. He was too busy rushing off because hey, that's what Harry does. If given the choice between sitting back and consulting his research when something dangerous is brewing, or charging in Staff Akimbo, Harry usually picked the Charge In approach.
Butters knows that's not his strong point. Oh sure he will go into danger if he has to, but he is far more useful as support and research. And now....with Bob, he has a huge reservoir of arcane lore and understanding to draw upon and apply to the fight.
So yeah, I think Butters will keep Bob for a while. Or at least I hope he does. I eagerly await the scene where Harry walks into Butters' place and sees all kinds of weird stuff laying around, and Butters gleefully showing off what neat magic thing they can do.
I mean really, given Butters Straight Man sense of humor, and Harry's Snark, the comedy value alone is golden.