Preheat the oven to 400 degrees F. Put a large colander inside a large bowl.
Melt 2 tablespoons butter in a large skillet over medium heat. Add a third of the squash to the skillet, arrange in a single layer and sprinkle with 1/2 teaspoon salt and a few grinds of pepper. Cook, tossing occasionally, until the squash begins to soften and are golden brown spots, about 5 minutes. Transfer to the colander. Repeat 2 more times using 2 tablespoons of butter for each batch and sprinkling with 1/2 teaspoon salt and few grinds of pepper. Transfer each batch to the colander.
Add 1 tablespoon butter to the skillet along with the pepper and onion and cook, stirring occasionally scraping up any brown bits, until the vegetables are soft, about 5 minutes. Add the garlic and cook, stirring, until fragrant, about 1 minute. Let cool for 5 minutes then fold into the squash. Transfer the mixture to a 2-quart casserole dish.
Whisk together the sour cream, eggs, 1/2 teaspoon salt and a few grinds of pepper in a large bowl. Fold in the Cheddar, thyme and chives. Pour over the squash making sure that some of the mixture sinks down to the bottom.
Microwave the remaining tablespoon of butter in a medium bowl until melted. Fold in the crackers and hot sauce. Sprinkle evenly over the squash. Bake until the eggs are cooked through and the crackers are golden brown, 30 to 35 minutes. Let sit for 10 minutes before serving.
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