Preheat the oven to 425°F (220°C). Boil the gnocchi according to the package directions, but pull them the moment they float.
Melt the butter in a saucepan over medium heat. Whisk in the flour and cook for 1 minute. Gradually whisk in the milk and simmer for 4 to 5 minutes, until thickened.
Remove from the heat and stir in the Parmesan and half the Gruyère until melted. Season with the thyme, salt, and pepper.
Combine the gnocchi with the sauce and pour into a baking dish. Lay the torn prosciutto pieces over the top, not mixed in.
Sprinkle the remaining Gruyère over the casserole. Toss the panko with the olive oil and scatter it evenly on top.
Bake for 20 to 25 minutes, until bubbling and the top is golden with crisp prosciutto edges.
Let rest for 5 minutes. Drizzle with the truffle oil and scatter chives over the top just before serving.