Preheat your oven to 400°F (204°C). Line baking sheets with silicone baking mats and set aside.
In a large skillet, heat the vegetable oil over medium heat and cook the thinly sliced onions with 1 teaspoon of salt until golden brown, about 30 minutes. Remove and transfer to a large bowl.
In the same skillet, sauté the mushrooms until tender, about 5 minutes. Remove and add them to the bowl with the caramelized onions.
Melt the butter in the same skillet and add the cubed apples along with the sugar. Cook until the apples are softened, about 10 minutes. Add to the bowl with the onions and mushrooms.
Stir in the grated Gruyere cheese, minced chives, and thyme. Mix well and season with salt and pepper to taste.
Roll out the thawed puff pastry and use a pizza cutter to cut it into 2-inch squares. Place the squares on the lined baking sheets.
Lightly brush each puff pastry square with beaten egg.
Place a tablespoon of the filling in the center of each puff pastry square.
Bake for 25 minutes, rotating the pans halfway through baking to ensure even browning. Bake until the puff pastry is golden brown and crisp.
Let the bites cool slightly before serving to avoid burning your mouth. Enjoy warm!