It was easy for him to tell when the personalities switched places. Hannibal realized that Jonathan was back before the words even escaped his lips.
"Don't apologize, Jonathan. If I had been offended or put off by it, I would have said something. I don't think it was a particularly great idea, but you can confidently tell Edward that it was Scarecrow who did it, and that it was nothing more than chaste and defiant."