Whisk together eggs and half-and-half in a large bowl. Pulse corn, in 2 batches, in a food processor until coarsely chopped, about 5 times. Add to egg mixture along with cheese, grated onion, flour, garlic, chives, thyme, salt, and pepper. Stir to combine. Transfer to a lightly greased 13- x 9-inch baking dish; cover and chill until ready to bake, up to 1 day ahead.

Preheat oven to 350°F. Remove casserole from refrigerator while oven preheats. Bake, uncovered, until golden and bubbly around edges and center is just set, about 45 minutes. Let stand 10 minutes before serving. Garnish with thyme and chives.