Preheat a 5- to 6-quart slow cooker according to the manufacturer’s instructions.
Season the chicken with salt and pepper. Place it in a large bowl or resealable plastic bag, add the flour, and toss to coat. Shake off any excess flour and place the chicken on a large plate or rimmed baking sheet.
In a 10- to 12-inch (25- to 30-cm) skillet over medium heat, cook the bacon until the edges are crisp, 10 to 15 minutes.
Using a slotted spoon, transfer the bacon to a paper towel-lined plate to drain. Reserve the fat in the skillet.
Add the mushrooms and garlic to the skillet and cook, still over medium heat, until golden brown, about 8 minutes. Transfer to the slow cooker.
Add 2 tablespoons oil to the skillet and heat over medium-high. Stir in the onions and carrots and cook until browned, 5 to 10 minutes. Transfer to the slow cooker.
Add the remaining 2 tablespoons oil to the skillet. Working in 2 batches, add the chicken thighs and cook over medium-high, turning once, until browned all over, about 8 minutes per batch. Using a slotted spoon, transfer the chicken to the slow cooker.
Pour off any excess fat from the skillet. Return the skillet to medium-high heat and carefully pour in the wine, scraping up the browned bits from the bottom of the skillet.
Bring the wine to a boil and then reduce the heat and gently simmer for 5 minutes.
Pour the wine and boiling water over the chicken in the slow cooker. Sprinkle with the cooked bacon and thyme. Cover and cook until chicken is tender, 5 to 6 hours on low or 2 1/2 hours on high.