At the end of White Night we learn that Bob can literally see Harry's soul. He can see that Harry lost some soul to Lash, and received some energy back from Murph in a hug or something. And we're supposed to believe that he couldn't see a spiritual entity growing inside Harry for years? That seems.... unlikely. So why did he never tell Harry about the spirit creature that could kill Harry if not dealt with properly?
I believe that it has to do with the future time travel. I think when future spirit-Harry comes back in time, he will have a talk to Bob and order him to never tell his self about the creature. But here's my question, do you think Bob will be able to talk about it now that Bonnie is out? If so, that might give away that he was ordered, which would give away time travel Harry, so I doubt that he will bring it up. (probably told to not do anything to give away time-travel Harry's actions) But how good is he at bluffing?
I suspect the knights might sit this book out, so since Butters still has Bob, we might not see him this book, but its an interesting thought. I think there is no way at all that Bob doesn't know about Bonnie.