Preheat broiler. Arrange chiles in a single layer on a baking sheet and broil until charred on all sides, turning chiles as necessary. Wrap in foil and let sit 15 minutes. Remove charred skin, stems, and seeds. Chop chiles and set aside.
Preheat oven to 375°. Heat oil in a large frying pan over medium-high heat, add onion and 1 tsp. salt, and cook, stirring, until onion is soft. Add tortillas and stir to coat. Transfer onion-tortilla mixture to an 8- by 8-in. baking pan. Sprinkle half the chopped chiles and half the queso fresco on top.
In a small bowl, whisk egg yolks with flour. In a large clean bowl with a clean whisk or beaters, beat egg whites and remaining tsp. salt until soft peaks form. Fold egg whites into egg yolk mixture; spread half on the casserole. Sprinkle remaining chiles on top. Spread remaining egg mixture over chiles and sprinkle with remaining queso fresco. Bake until golden and puffy, 20 to 25 minutes. Sprinkle with cilantro and serve with hot sauce.
Note: Nutritional analysis is per serving.