Combine red wine and chicken stock in a large mixing bowl (metal or glass) and add chicken. Arrange it so chicken is mostly covered and set aside.
Prepare all the vegetables, dice bacon, and measure remaining ingredients.
Sear bacon and chicken:
Preheat a large Dutch oven over medium-high heat and add oil. Add diced bacon into the pot and cook it until bacon is crispy.
While bacon is cooking, take chicken out of the wine mixture, let all excess wine drip off back into the bowl, and pat the chicken dry with a paper towel. Place chicken on a cutting board and season it with salt and pepper on all sides.
Take out the crispy bacon pieces and set them aside. Leave bacon grease in the pot.
Sear chicken in the pot in batches so it doesn't get overcrowded. Sear it skin side down first for a few minutes and then turn it over and sear on the other side until golden brown.
Take seared chicken out of the pot and set aside.
Add sliced onion and carrots into the pot, mix, and let them sear for a few minutes undisturbed, until start to golden.
Add mushrooms, stir, and sear until all vegetables started to get golden.
Make a little well in the center and add pressed garlic. Sauté for a few seconds, until it's fragrant.
Pour in cognac, let it simmer, and stir everything together.
Add chicken back into the pot.
Whisk in tomato paste into the wine mixture in a measuring bowl and pour the mixture into the pot.
Add pearl onions, some more salt and pepper and thyme sprigs.
Lower the heat to medium and being the mixture to simmer. Simmer for 10-15 minutes.
Lower the heat to low. Cover the pot with a lid but leave a small crack for steam to escape. Cook the chicken for about an hour.
Take chicken out of the pot carefully and set aside.
In a small bowl, mix together softened butter and flour with a fork by mashing it together and mixing until completely combined.
Stir the flour mixture into the pot until completely incorporated and let it simmer for a couple of minutes until thickened.
Return chicken to the pot and cook a couple more minutes for the chicken to heat through.
Take off heat and garnish with some fresh parsley.
You can sprinkle the crispy bacon on top of coq au vin as you serve it.