Preheat oven to 400 degrees. Place pastry rounds on a parchment-lined baking sheet and prick all over with a fork. Divide half the cheese among pastry rounds. Top each with 2 to 3 apple slices. Tuck 2 to 3 beet slices among apple slices and top with remaining cheese. Season with salt and pepper and sprinkle with thyme. Bake until pastry is golden brown and slightly puffed, 13 to 15 minutes. Serve warm or at room temperature.