In The Witch, in the middle of the night, the evil witch goes into the barn and attacks the goats. The next morning, we see the twins have disappeared.
Did the witch take the twins?
What happened to the twins is unknown since no explanation was given. In the scene after the night in the barn when one of the witches sucks (or whatever) the goats milk they are not visible. All one can do is assume they were taken by the witch or witches. And we already know what those witches do with babies and children. By the end of the film the witches have a lot to celebrate; dead Christians, 3 children to eat and a brand new young member of the coven.
Honestly this is my opinion, however the kid did say she was the witch of the forest whilst then with her twin that black Phillip whispers to them. They can may as well be apprentices to black phillip..the goat said he will guide your hand would he also guide you as well? He did go Tomuson or whatever her name was. Nonetheless its unfortunate that you don't see them again.