Preheat oven to 350 degrees. Bring chicken broth to a boil in a small saucepan then add rinsed and drained quinoa. Place a lid on top, turn heat down to medium-low, and then simmer until all the broth has been absorbed and quinoa is tender, about 15 minutes. Set aside to cool slightly (can be done ahead of time.) Meanwhile, melt butter in a large skillet over medium-high heat then add mushrooms and shallots, season with salt and pepper, and then saute until mushrooms are golden brown and tender, 5-7 minutes. Add garlic and dried thyme then saute for another minute. Set aside to cool slightly (can be done ahead of time.) In a large bowl combine cooked quinoa and mushrooms, swiss cheese, parmesan cheese, and whisked eggs then stir to combine. Spray a 24 count mini muffin tin extremely well with nonstick spray then spoon mixture to the top of each cup. Place muffin tin on top of a baking sheet then bake for 18-22 minutes, or until light golden brown on top. Let cool in tins then store in an airtight container in the refrigerator for up to 5 days. To freeze: Place cups on a baking sheet then freeze until solid, and then transfer to a freezer bag. Place frozen cups on a plate then top with a paper towel and microwave for 20-40 seconds to reheat.