Melt butter in a medium saucepan over medium-high heat. When bubbling, add flour. Reduce heat slightly and cook, stirring, until roux is pale blonde and smells nutty, about 5 minutes. Slowly add milk, whisking to incorporate. Run a rubber spatula around saucepan edges to remove any flour clumps. Bring to a gentle simmer, and cook 10 minutes. Add Comté cheese, and stir until melted. Add salt and pepper to taste.

Preheat oven to 350°F. Cook pasta in well-salted boiling water in a large stockpot according to package instructions, until just shy of al dente. Drain, cover, and set aside.

Combine ⅔ cup crumbled bacon (reserve ⅓ cup for topping), tuna, sun-dried tomatoes, and farfalle. Add cheese sauce and mix well. Pour into a lightly greased 3-quart casserole dish, and top with Cheshire cheese.

Bake 30 minutes, until top is golden brown. (Broil for 1 to 2 minutes, if necessary.) Top with reserved crumbled bacon and chives. Let cool 10 minutes before serving.