Toss shredded cheeses, flour, and pepper together in a small bowl. Set aside.
Combine milk, cream cheese, 1/3 cup green onions, hot sauce, and chopped jalapenos in a 9×13-inch baking dish. Add corn and shredded cheese mixture; stir until well combined.
Cover and bake at 350 degrees for 30 minutes. Uncover, sprinkle with remaining 1/3 cup green onions, and bake 5 minutes more.
Sprinkle with chopped cilantro, if desired, just before serving.
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