Caleb still doesn't follow. If both were wiped then where did the new person come from? That's not how DID works. But that's fine, he doesn't have to get it.

"I'm sorry for your loss." He is very genuinely sorry, regardless of how it works, Barry lost a friend. "It's good that you're taking time to process, before deciding what to do."

He knows there's a Caitlin in Duplicity, and he figures she does not know about this third person. So Barry has to deal with that loss and also decide what to tell her.