Preheat the oven to 350 degrees F.
Melt 3 tablespoons butter in a large skillet over medium-high heat. Add the onions and sprinkle with 1 teaspoon salt and 1/2 teaspoon pepper and cook, stirring occasionally, until the onions are very soft and just begin to brown, about 20 minutes. Add 1 tablespoon thyme and cook for an additional minute. Set aside.
Meanwhile, bring a large pot of salted water to a boil. Cook the noodles according to the package directions. Reserve 1/2 cup of the pasta water. Drain the noodles and return them to the pot.
While the noodles are still warm, add the cooked onions, sour cream, cream cheese, reserved past water and 1/2 cup Gruyere. Stir until the sauce is smooth and creamy and coats the noodles. Fold in the chicken. Season with salt and pepper. Transfer to a 2-quart baking dish.
Microwave the remaining 5 tablespoons butter in a medium microwave-safe bowl until melted. Add the fried onions, breadcrumbs, remaining 1/2 cup Gruyere and 1 tablespoon thyme to the butter and toss until the breadcrumbs are coated. Sprinkle the buttered breadcrumb mixture evenly over the noodles to cover completely.
Bake until the topping is golden brown, 35 to 40 minutes.
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