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1
Preheat oven to 375 degrees F (190 degrees C).
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2
Bring water to a boil in a saucepan; remove from heat and stir couscous into the water. Cover saucepan and let stand until water is absorbed completely, 5 to 10 minutes. Fluff couscous with a fork.
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3
Heat olive oil in a large skillet over medium heat; cook and stir onion in hot oil until onion starts to soften, about 5 minutes. Transfer 1/2 of the onion to a large bowl.
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4
Pour marinara sauce, beef broth, balsamic vinegar, and red pepper flakes into skillet with remaining onion; cook and stir until heated through, about 1 minute. Pour marinara mixture into a 9x13-inch baking dish.
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5
Stir vegan beef crumbles, diced tomatoes, parsley, garlic, black pepper, and cayenne pepper into onions in the large bowl until well-mixed. Add couscous and 3/4 of the Parmigiano-Reggiano cheese and stir until filling is well-combined. Stuff each pepper half with couscous mixture and place stuffed peppers in marinara sauce in the baking dish. Sprinkle remaining Parmigiano-Reggiano cheese over peppers and cover the baking dish with aluminum foil.
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6
Bake in the preheated oven for 45 minutes. Remove aluminum foil and continue baking until peppers are tender and cheese is browned, 20 to 25 minutes more.