In a large bowl toss together onion, carrot, celery and garlic cloves. Spread half the mixture into a large, shallow baking dish.
Top vegetables with a single layer of chicken pieces and sprinkle remaining vegetables over chicken. Top with 2 thyme sprigs.
Pour wine over chicken mixture until completely submerged.
Tightly wrap the chicken mixture and refrigerate for 12 to 18 hours.
Preheat oven to 325˚F.
Pour oil into a large Dutch oven and place over medium-high heat.
Add pancetta and fry for 2 to 3 minutes or until light and crisp. Remove from heat with a slotted spoon and set lardons aside.
Remove chicken from marinade and pat dry. Season with salt and pepper and add pieces into the Dutch oven skin side down, searing the pieces on each side for 2 to 3 minutes. Remove from pot and set aside.
Drain all but 1 ½ tablespoons grease from the pot and drain vegetables from the marinade. Pour marinated vegetables into the pot and sauté for 3 to 4 minutes. Add cippollini onions and continue to sauté for 2 to 3 minutes.
Add 2 cups of the marinade liquid into the pot and top with chicken stock.
Nestle the chicken pieces back into the pot, skin side up, and top with remaining thyme sprigs. Season with salt and pepper, cover and place into the oven for 45 to 55 minutes or until the chicken has cooked through completely.
Remove the pot from the oven and strain 1 cup braising liquid. Pour the strained liquid into a saucepan and simmer for 2 to 3 minutes.
In a small bowl, mash together the butter and flour and whisk the mixture into the simmering liquid. Continue to simmer and whisk until the mixture thickens and is smooth. Lightly season with salt and pepper.
To assemble: Place a couple pieces of chicken into each bowl and top with 3 to 4 onions. Drizzle some of the thickened sauce over each dish and finish with a small sprinkle of lardons and fresh thyme. Season with salt and pepper and serve.