Preheat the oven to 350°F. Spray a 9x13-inch baking dish with cooking spray then set it aside. Melt the butter in a large skillet over low heat then add the onions and allow them to soften and begin to caramelize.
Add the kielbasa and minced garlic to the skillet and allow it to brown. Stir frequently to make sure the onions don’t get too dark. About 3-4 minutes.
Sprinkle the flour over the onions and kielbasa until it is fully absorbed. Slowly pour the chicken broth and gently stir until the sauce begins to thicken. Stir in the ground mustard, paprika, pepper and salt until combined.
Remove the skillet from heat and add the sour cream, 1 cup of sharp cheddar and the mozzarella cheese. Gently stir until the cheese is melted.
Add 12 pierogi into the bottom of the baking dish. Gently spread half of the kielbasa and sauce over the pierogi layer.
Layer the remaining 12 pierogi and then pour the remixing kielbasa and sauce, spreading out evenly.
Top with the remaining shredded cheddar. Cover the dish with aluminum foil tightly and place in the over for 25 minutes.
Remove the foil and continue to cook for 10-15 minutes until the casserole is bubbling and the cheese is melted.
Allow the casserole to set for a few minutes, then sprinkle the sliced green onions over the top. Serve and enjoy.