Preheat the oven to 375 degrees F.
Bring a large pot of salted water to a boil. Add the macaroni and boil until the pasta is cooked, 8 to 10 minutes.
In a medium saucepan, combine the flour and butter. Cook 5 minutes over medium heat while whisking. Add the milk and bring to a simmer, continually whisking. Cook over low heat, 10 minutes.
Slowly add the cheeses and continue whisking until melted. Add the lobster stock, cognac, hot sauce, nutmeg and salt and pepper, to taste. Remove from the heat and set aside until needed.
In a large bowl, mix the cooked pasta, Cheese Sauce, lobster, scallions and chives. Place in a baking pan and cover the top with the mixed cheeses. Bake until the top is browned, about 30 minutes. Remove from the oven and garnish with fresh chives.
This recipe was provided by professional chefs and has been scaled down from a bulk recipe provided by a restaurant. The Food Network Kitchens chefs have not tested this recipe, in the proportions indicated, and therefore, we cannot make any representation as to the results.