Place the lima beans into a large container and cover with several inches of cool water; let stand 8 hours to overnight. Drain and rinse.
Preheat an oven to 400 degrees F (200 degrees C). Drain the soaked lima beans and cook according to package directions.
Blend the cooked lima beans and milk together in a blender until smooth; season with salt. Set aside.
Heat the olive oil in a large skillet over medium heat; cook the onion in the hot oil until soft, about 5 minutes. Add the chicken and cook until completely browned, 7 to 10 minutes more. Stir the zucchini, tomato, cumin, and cayenne pepper into the chicken; cook until the vegetables are slightly tender, about 7 minutes more. Spread the mixture into the bottom of an 11×7-inch baking dish; pour the lima bean mixture over the chicken and vegetables in a single, smooth layer. Top with mozzarella and Parmesan cheese.
Bake in the preheated oven until the top is browned and crisp, about 10 minutes.