Preheat the oven to 400˚F.
Cut the spiralized noodles in half. Place them on a baking sheet and toss with the olive oil. Bake for 5-7 minutes, or until they can be easily pierced with a fork. Set aside.
Meanwhile, in a large saucepan, melt the butter on medium heat. Add in the coconut flour and whisk until it forms a thick paste. Add in the milk and combine until thickened.
Once thickened, add in the butternut squash noodles. Mix in the cheeses and stir to combine. Once the cheeses have melted, divide into bowls.