In a 10 to 12inch saute pan, heat butter until foam subsides. Add onions and cook slowly until soft and golden brown, about 12 to 15 minutes. Allow to cool.
Butter the flan molds and preheat oven to 350 degrees.
Divide the onions among the flan molds. In a bowl, whisk together nutmeg, rosemary, milk, eggs, yolks and grated cheese. Season with salt and pepper and divide milk mixture among the flan molds. Place flans in brownie pan and fill to halfway with cool water. Place in oven and bake 45 minutes, or until insides are set or a toothpick exits dry. Remove from oven and allow to cool 5 minutes. Unmold and serve with fonduta and truffles.