When Ed and Lorraine Warren are returning from the Perron's, their daughter Judy is haunted by the Witch Spirit. She comes down to see the witch sitting in the chair with the Annabelle doll. We can see her stroking or grooming the doll. The doll then turns around to look at the Judy standing at the door.
What was the Witch Spirit Bethsheba from the Perron's house doing with the Annabelle doll in the Warren's house?
The spirit of Bethsheeba had latched on to the necklace which Lorraine had dropped in the basement of the Perron's house. My guess is that, it created a connection with the necklace's pair that was at the Warren's house (remember the violently shaking necklace in Judy's room?!). This explains the presence of Bethsheeba's spirit at the Warren's.
Now to explain, what was she doing with the Annabelle doll, you'll have to go back a little to the scene where Lorraine was combing Judy's hair sitting at the very same spot, in the very same chair! This is what Bethsheeba is imitating.
Why is she doing that?!
I have no clue! After all, the activities of evil spirits aren't really logical. They do whatever they do to spook and scare the crap out of you. And I'd say she was pretty successful at that. However, she was a twisted soul who tried to kill its own offspring and that of others. The mother-child relation wasn't sacred to her, and I guess she derived some kind of pleasure mocking it.
