Preheat your oven to 350°F and grease a casserole dish with nonstick cooking spray.
In a large pan, melt half the butter over medium heat. Add the diced onion and sliced squash along with the thyme, ½ teaspoon of salt, and ¼ teaspoon of pepper. Sauté for about 5 minutes, until the onion and squash have softened. Remove from heat and let cool.
In a large bowl, whisk together the sour cream, mayonnaise, eggs, half the cheddar cheese, and a pinch of salt and pepper.
Add the cooked squash and onion to the sour cream mixture and mix until well combined.
Pour the mixture into the prepared casserole dish.
Melt the remaining butter. Crush the crackers until they form coarse crumbs, then mix with the melted butter and Parmesan. Sprinkle evenly over the casserole.
Bake for 20–25 minutes, or until the casserole is set and the topping is golden brown. Sprinkle the remaining cheddar cheese on top as soon as it comes out of the oven.