Preheat the oven to 375°F.
Cook the jumbo pasta shells according to package instructions until al dente. Drain and set aside.
In a large skillet, heat the olive oil over medium heat. Add the chopped onion and sauté for about 3 minutes until softened.
Stir in the minced garlic and cook for an additional minute until fragrant.
Add the sliced mushrooms, thyme, salt, and black pepper to the skillet. Cook for about 5-7 minutes, stirring occasionally, until the mushrooms are tender and any liquid has evaporated. Remove from heat and let cool slightly.
In a mixing bowl, combine the ricotta cheese, half of the mozzarella cheese, Parmesan cheese, and chopped parsley. Stir in the cooled mushroom mixture until well combined.
Spread a thin layer of marinara sauce on the bottom of a 9x13 inch baking dish.
Stuff each cooked pasta shell with the mushroom and cheese mixture and place them in the baking dish.
In a small bowl, mix the heavy cream with the remaining marinara sauce. Pour the cream mixture evenly over the stuffed shells.
Sprinkle the remaining mozzarella cheese on top.
Cover the baking dish with aluminum foil and bake for 25 minutes.
Remove the foil and bake for an additional 10-15 minutes until the cheese is bubbly and golden.
Let the dish cool for 5 minutes before serving.