Preheat the oven to 425 degrees F. Remove the stems from 24 large cremini mushrooms.
Wipe the caps clean with a damp paper towel, then toss with 2 tablespoons olive oil and season with salt. Arrange on a baking sheet.
Melt 3 tablespoons butter in a large skillet over medium heat. Add 2 thinly sliced onions and 2 teaspoons chopped thyme; season with salt and pepper and cook, stirring, until the onions are caramelized, about 20 minutes. Add 1/4 cup red wine; cook until evaporated, 1 minute. Add 1/2 cup beef broth; simmer until the onions are glazed, 3 minutes. Sprinkle breadcrumbs inside the mushroom caps; fill with the onion mixture, then sprinkle with 1 cup shredded gruyere and 2 tablespoons grated parmesan.
Bake until the mushrooms are tender and the filling is golden, 15 to 17 minutes. Let cool 5 minutes, then remove from the baking sheet. Top with parsley.