Bring a large pot of salted water to a boil and cook the pasta shells according to package directions for al dente. Drain and run under cold water until cool enough to touch.
Mix the ricotta, 1 cup of the Italian blend cheese, the red pepper flakes, lemon zest, 1 pinch of the nutmeg, 1/2 teaspoon salt and a few grinds black pepper together in a medium bowl. Set aside.
Heat the olive oil in a large heavy-bottom pot over medium-high heat. Add the chicken, 1/2 teaspoon salt and a few grinds black pepper and cook, stirring occasionally, until the chicken is just cooked through, 5 to 6 minutes. Transfer to a plate and add the leek to the pot. Cook, stirring occasionally, until softened, 3 to 4 minutes.
Pour the wine into the pot and stir to scrape up any browned bits with a wooden spoon. Bring to a boil and reduce until completely evaporated, stirring. Lower the heat to medium, pour in the cream and bring to a simmer. Stir in the Parmesan, the remaining pinch nutmeg, 1 teaspoon salt and a few grinds black pepper. Remove from the heat.
Fold the chicken and its juices from the plate into the ricotta mixture. Spread 1 cup of the cream sauce onto the bottom of a 9-by-13-inch casserole dish. Fill each pasta shell with a spoonful of ricotta mixture. Arrange the stuffed shells, seam-side up, shingling them so they all fit (you should have 5 shells along the short side and 6 shells along the long side). Ladle the remaining sauce over the top, then sprinkle with the remaining 1 cup Italian cheese blend and cover with aluminum foil.
Bake until the cheese is melted and the sauce is bubbling, about 20 minutes. Remove the foil and continue to bake until the cheese and tops of noodles start to turn golden brown, 15 to 20 minutes. Let cool for 10 minutes before sprinkling with some chives and more red pepper flakes.
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