Add chicken to a 1-gallon zipper-lock bag. Pour in one cup red wine and seal bag, pressing out air. Let stand while you prepare the remaining ingredients or overnight for the best results.
Preheat oven to 350°
In a large Dutch oven or rondeau, cook bacon over medium-high heat, stirring and reducing heat as necessary to prevent scorching, until browned and fat has rendered, about 10 minutes. Remove from heat and, using a slotted spoon, transfer bacon to a paper towel-lined plate.
Remove chicken from zipper-lock bag, discard wine, and pat dry.
Season chicken with salt and pepper. Return Dutch oven with rendered bacon fat to medium-high heat. Add chicken thighs skin-side down, and cook until browned, about 7 minutes. Turn and brown the other side, about 5 minutes. Don't move the chicken around while cooking, allow it to sear in place. Use a spatula to get under the chicken when turning being careful not to rip the skin.
Remove Chicken from pan setting aside until needed
Add mushrooms to pan and cook over medium-high heat, stirring frequently, until browned, 10 to 12 minutes. Add onions, carrots, and garlic and cook, stirring, until lightly browned, about 5 minutes. Add bacon, the remainder of the wine, tomato paste, chicken stock, thyme and rosemary and bring to a simmer, stirring up any browned bits.
Add chicken back to pan, leaving skin side up and not submerged if possible. Transfer to oven and cook, uncovered, for 1 hour.
Remove pan from the oven and take the chicken out of the pan.
Add in two tablespoons of unsalted butter that has been rolled in flour, getting as much flour into the butter as possible. This is called a beurre manie and will thicken your sauce. Mix the beurre manie in well and allow to simmer over medium heat.
Return chicken to pot, spooning sauce on top. Garnish with remaining sprig of thyme or rosemary. Serve with potatoes, pasta, or rice.