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Preheat oven to 350°F. Coat a 9-by-13-inch baking dish with cooking spray.
Bring a large pot of water to a boil. Cook noodles until not quite al dente, about 2 minutes less than the package directions. Drain; return the noodles to the pot and cover with cool water.
Melt butter in a Dutch oven over medium heat. Add leeks; cook, stirring often, until softened, about 6 minutes. Sprinkle flour over the leeks; stir well. Cook, stirring constantly, for 2 minutes. Whisk in milk in a slow stream and cook, whisking constantly, until thick and bubbling, 8 to 10 minutes. Whisk in thyme, salt, nutmeg and pepper. Remove from the heat.
Assemble lasagna in the prepared baking dish by layering one-third of the noodles, one-third of the sauce, half the squash, one-third of the cheese, half the remaining noodles, half the remaining sauce, all the pine nuts, all the remaining squash, half the remaining cheese, all the remaining noodles, all the remaining sauce and all the remaining cheese. Cover with parchment paper then foil.
Bake the lasagna for 50 minutes. Uncover and bake until bubbling and lightly browned, 30 to 45 minutes more. Let stand for 10 minutes before serving (or follow make-ahead instructions).