In a medium, microwave-safe bowl in the microwave or in small saucepan on the stove, melt the butter. Set aside to cool to room temperature. Place a rack in the center of the oven and preheat to 350 degrees F. Lightly coat a 9x13-inch baking dish with nonstick spray.
In a medium bowl, whisk together the flour, cornmeal, baking powder, salt, pepper, and thyme.
In a large bowl, whisk together the eggs, honey, drained whole kernel corn, creamed corn, Greek yogurt, and melted, cooled butter. Stir in 3/4 cup of the shredded cheese and the chives.
Add the dry ingredients to the wet ingredients and with a rubber spatula or wooden spoon, stir gently just until the flour disappears.
Pour batter into the prepared baking dish and spread it into an even layer. Sprinkle the remaining ¼ cup cheese evenly over the top .
Bake the corn casserole for 50 minutes. Increase the oven temperature to 400 degrees F and continue baking until the cheese is a gorgeous golden brown, about 5 to 8 minutes more. Let rest 10 minutes prior to serving.
Notes
TO STORE: Let the corn casserole come to room temperature, and place in an airtight storage container in the refrigerator for up to five days.
TO REHEAT: Rewarm leftovers in oven at 350 degrees F until warmed through, or rewarm gently in the microwave.
TO FREEZE: To freeze entire casserole, double wrap with plastic wrap and then foil. Or freeze leftovers in a freezer-safe, airtight container. Let thaw overnight in fridge before reheating.