Wouldn't canon be that Bob has no memories of his period with Kemmler having given them to Evil Bob when he split off.. And Evil Bob seemed to have no memories of Kemmler's last stand.
I need to go back and read Ghost Story, and I could be totally wrong, but it seems like Harry inadvertently created Evil Bob when he ordered Bob to "forget" everything that happened while he was in the possession of Kemmler. This was of course after Harry had ordered Bob to remember back in Dead Beat and "Kemmler Bob aka Evil Bob," nearly killed him.. It scared Bob as well I think, so he forgot so well that Evil Bob was born. And now, I think you are right, Bob has no more memories of that time.
It worked for Kemmler, and of course Bob would know.
Still limited, the Wardens did successfully get him in the end.