Preheat the oven to 375°F. Melt butter in a medium saucepan over medium-high heat. Add chopped onion and cook 2 minutes until it starts to soften. Add sausage and cook until it starts to brown, about 10 minutes. Add thyme and diced apples and cook 5 minutes.
Next, add flour and stir to combine evenly. Add cider and cook about 2 minutes to allow alcohol to start to cook down, then add milk. Cook and stir occasionally, until mixture begins to thicken, about 8-10 minutes longer. Slowly stir in half of each cheese, add salt and pepper, and cook until the cheese has melted.
While the sauce mixture is cooking, bring a large pot of salted water to a boil. Add pasta and cook, stirring occasionally, until barely al dente, about 5 minutes. Drain pasta, transfer to cheese sauce, and stir well to coat.
Spread pasta into a lightly greased 9x13-inch baking dish and top with remaining half of cheese. Place dish on a baking sheet and bake until golden brown and bubbly, about 45 minutes. Let cool for 10 minutes before serving.