Preheat oven to 375 °F. Line a baking sheet with parchment.
Cut a crosshatch pattern into the sourdough boule without slicing through the bottom.
Brush melted butter evenly into all crevices.
Stuff apple slices and shredded cheddar into the cuts.
Loosely wrap the loaf in foil and bake for 15 minutes. Unwrap and bake an additional 8–10 minutes until cheese is bubbly and golden.
Drizzle hot honey over the bread, finish with flaky sea salt and fresh thyme leaves and serve immediately.