01Preheat oven to 400F. Line baking sheet with parchment paper.
02Melt 2 tablespoons butter in large skillet over medium-high heat. Stir in sliced onion one handful at a time until well coated in butter. Stir in pinch of salt. Reduce heat to medium-low and continue to cook, stirring occasionally until onions are deep golden brown, 30-40 minutes. Stir in thyme. Remove onions from skillet and set aside.
03Add remaining butter, apple slices and pinch of salt to same skillet over medium heat. Cook, stirring frequently, until apples are just tender, about 10 minutes.
04Scatter cheddar over flatbread and top with caramelized onions. Top onions with apples and brie. Bake on prepared baking sheet until flatbread is golden and cheese as melted, 10-12 minutes.
05Remove from oven and drizzle with 1-2 teaspoons of honey before serving.