Step 1

Preheat oven to 375°F. Combine shallots, vinegar, 1/2 cup water, sugar, and 1 teaspoon salt in a microwavable bowl. Microwave on HIGH 3 minutes. Let cool 15 minutes; drain.

Step 2

While shallots cool, melt butter in a Dutch oven over medium. Whisk in flour; cook, stirring constantly, until light golden brown, about 2 minutes. Gradually whisk in warm milk until combined. Increase heat to medium-high; bring to a boil. Reduce heat to medium-low; simmer, whisking often, until thickened, 6 to 8 minutes. Remove from heat. Add Gruyère, pepper, nutmeg, and remaining 1 teaspoon salt; stir until cheese melts. Stir in pasta and 3/4 cup pickled shallots.

Step 3

Transfer pasta mixture to a 13- x 9-inch baking dish. Sprinkle remaining pickled shallots over top of pasta; sprinkle evenly with raclette cheese. Bake in preheated oven until top is golden brown, about 35 minutes. Garnish with chives.