After the scene with his 'birthday', when he goes up the stairs he's very weary of the attic, this should show up at several points before Hobbes starts talking and the flashback starts. Perhaps we can have a transition where he goes up to the puddle leaking from it and almost gets pulled out of it, and when he transitions out (Hobbes saves him) he's in a different place and Rosalyn tells him he must have fallen asleep, but when he looks at his arm the bruises from the finger nails are still there. Or maybe we use it to transition directly to the conversation with Hobbes, because he can 'wake up' in his room, leaning against the wall and then open the drawer and try to talk to Hobbes again (or perhaps Hobbes is lying dumbly on his bed, which Calvin never uses).
Before the flashback we should hint to the monster in his attic. When he goes upstairs he finds at dripping or something and is careful to avoid it, perhaps his attic door is open with dripping coming into a puddle underneath, he slides past it and the camera pans to the darkness and perhaps some whispering, he quickly slides by and rungs into his room and slams the door behind him, we can hear bumping overhead.
I'm thinking that in this scene Hobbes can say the introduction that he always says whenever he's reborn, perhaps about being a new best friend. Calvin corrects him "We've met before. Quite a few times actually." or something like that. Hobbes can reply something like "We have? We have..." as if realizing it. I dunno, that's kind of weak sounding, but it makes sense for Hobbes to have his memory wiped again until Calvin allows him to remember. (Play around with it.)