01 -
Preheat oven to 350°F and grease an 11 x 7-inch baking dish with cooking spray.
02 -
Melt 3 tablespoons butter in a large skillet over medium-high heat. Add squash, onion, and 1 teaspoon salt. Cook, stirring often, until squash is tender and liquid has evaporated, about 10 minutes.
03 -
Transfer cooked squash mixture to a colander set over a bowl. Let drain for 5 minutes and discard any excess liquid.
04 -
In a large bowl, stir together eggs, sour cream, Cheddar, Swiss, mayonnaise, thyme, pepper, and remaining 1 teaspoon salt. Gently fold in drained squash mixture.
05 -
Spoon the squash mixture into the prepared baking dish, spreading evenly.
06 -
Microwave remaining 3 tablespoons butter in a bowl until melted, about 25 seconds. Toss with crushed crackers and Parmesan until combined.
07 -
Sprinkle cracker mixture evenly over the squash filling. Bake until golden brown, about 20 minutes.