“I don’t remember very much of it.”
"Bob. You never forget anything.”
“No,”Bob said. His voice shrank into something very small. "Unless I want to, Harry.”
“You’re saying that you chose to forget things about Kemmler.”
“Or was compelled to,” Bob said.
Based on this, Bob isn't sure who had him forget Kemmler. He just knows he forgot.
“Too late! Whatever you have done to my thoughts, the master will not be pleased that you have meddled with his servant.” ... “Do you know how long I’ve been waiting for that?” the spirit purred, drifting back and forth over me. “Sitting there locked behind my own thoughts? Waiting for the chance to fight free? Finally, you thick-witted ogre, I get to leave your stupidity behind.”
Based on what Evil Bob said in Dead Beat, we can surmise that he knows everything Bob knows (including that DuMorne was killed). We can also surmise that Evil Bob still thinks Kemmler is alive, and that he too doesn't know who made him forget. Which is interesting, because you'd think one or the other would know if they did it, of their own volition or by someone else's.
It suggests that someone might have had Evil Bob suppressed, and had both versions forget why it was done. Talk about double secret probation.
Harry clearly didn't do it.
DuMorne-DuMorne could have, but why would he have both Bob's forget the order? He might have wanted some but not all of Kemmler's knowledge for himself, and wouldn't want to deal with Evil Bob's attitude all the time. But why forget the forgetting?
Kemmler-DuMorne could have, but why bother? He would want to keep his assistant intact to continue helping him. I could see him maybe wanting to seal the more dangerous stuff away, in case Harry or Elaine came across the skull. But again, why forget the forgetting? He could have easily told Evil Bob that it was a precaution.
Kemmler-Kemmler has a good reason to seal Evil Bob away. If he knew the Council Wardens were about to catch him, he wouldn't want his secrets to be easily revealed. But you'd think he'd put better safeguards in place to keep people away from the knowledge. Otherwise when Bob says he doesn't recall, they'd ask him to try, and then Evil Bob would be there.
Maybe forgetting the forgetting was an extra precaution to lower the odds that someone would ask the right thing to bring Evil Bob back?