Preheat your oven to 425 degrees. Spray a baking sheet with non-stick cooking spray. Place the potatoes on the baking sheet and using a fork pierce the potatoes. Next, rub the potatoes with olive oil, salt, and pepper. Cook the potatoes for 25 minutes and then flip. Continue to cook for another 25 minutes or until tender.
Meanwhile, make the French Onion filling. In a large skillet preheated to medium-heat, melt the butter. Add the onions, thyme, salt, and pepper. Stir to combine and cook the onions until caramelized, about 15 to 20 minutes.
Next, add in the flour and garlic, and cook until fragrant. Pour in the beef broth, Worcestershire sauce, and stir. Bring the mixture to a simmer. Let the onion mixture simmer until slightly thickened about 5 to 10 minutes. Add more salt and pepper if desired.
When potatoes are cooked, cut a slit lengthwise on the top of the potato, then press ends together to create an opening. Spoon the French onion soup mixture into each potato and top with shredded gruyere. Place on a prepared baking sheet and bake until cheese is melted. Garnish with more thyme sprigs if desired and serve.