Season chicken thighs with salt and pepper, then cook in a large Dutch oven over medium-high heat until browned on both sides, about 5 minutes per side; remove and set aside.
Add chopped bacon to the same pot and cook until crispy; remove bacon with a slotted spoon and set aside, leaving drippings in pot.
Add mushrooms and pearl onions to the pot and cook until browned, about 6 minutes; add garlic and cook 1 minute more.
Stir in tomato paste, then add wine, chicken broth, bay leaves, and thyme; bring to a simmer.
Return chicken and bacon to pot, cover, and simmer for 30 minutes until chicken is cooked through and tender.
In a small bowl, mash together butter and flour to make a paste; stir into the sauce and simmer 5 more minutes until thickened.
Remove bay leaves, adjust seasoning with salt and pepper, and garnish with fresh parsley before serving.