Preheat the oven to 350°F.
Season thighs well on both sides with lemon pepper. Place the flour in a shallow dish. Then dredge the chicken in the flour and place on a separate plate.
In a deep oven proof skillet or dutch oven, add oil and heat over medium-high heat. When the oil is hot but not smoking, add the thighs and brown well on both sides, about 5 or 6 minutes. Remove the chicken from the skillet and set aside.
Add the onions to the oil and cook, stirring to scrape up any browned bits at the bottom of the pan. Cook for about 5 minutes. Add the garlic, and season with salt and pepper. Cook for another minute or two. Add the wine, lemon juice, and chicken broth. Let mixture simmer for a few minutes. Add the butter and allow it to melt.
Add the chicken thighs to the sauce. Top with chopped chives. Cover with lid, and place in the middle of the oven. Bake for 20 minutes, remove the lid and cook an additional 20 minutes. Before serving sprinkle with a garnish of fresh chopped chives and the ¼ cup of Parmesan cheese.