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Season the chicken pieces liberally with salt and pepper, then brown in 2 batches on both sides, and remove to plate. Add the onions, carrots, thyme, and bay leaves, and season with salt and pepper. Cover the pan and sweat the vegetables 5 to 6 minutes, stirring occasionally, until softened. Add the flour and stir 1 to 2 minutes, then add the cider, syrup, vinegar, and 1 cup stock, stirring between each addition. Slide in the potatoes, and apples, and sprinkle the bacon over the top. Nest the chicken into the pan and add more stock until the liquids reach the edge, but do not cover the chicken. Cover the pan, reduce the heat, and cook the chicken through, 15 minutes or so. Cool completely, and store for a make-ahead meal.
Reheat in an oven preheated to 325 degrees F, or on the stovetop over medium heat, covered until warmed through. Once hot, serve immediately. Remove the cooked chicken to a serving platter or shallow bowls, stir to thicken and combine the sauce and vegetables, and spoon over and around the chicken.