Preheat oven to 400 degrees. Prick sweet potatoes with a fork. Place on a rimmed baking sheet and bake until tender, about one hour.
Meanwhile, heat oil in a saucepan over medium heat. Add garlic and cook for 30 seconds. Add chipotle chiles, beans, quinoa, vegetable broth and salt and cook for 10 minutes. Stir in lime juice.
Make Creamy Lime Sauce by combining yogurt, garlic, lime zest, lime juice and sea salt in a small bowl.
Split potatoes and remove flesh, leaving ½ inch in tact. Mash in a medium bowl and stir in quinoa mixture. Sprinkle with cheese and return to oven until melted, about 5 minutes. Top with Lime Sauce and cilantro and serve warm.