In a large, heavy sauté pan, cook the bacon over medium-high heat until crisp and the fat is rendered, 4 to 5 minutes. Transfer bacon to a plate lined with paper towels and drain all but 2 tablespoons of fat from pan. Return the pan to the heat.
Season the chicken on both sides liberally with the Chicken Rub. Dredge in the flour to coat lightly, shaking to remove any excess.
Add the chicken to the fat in the pan and cook over medium-high heat until golden brown on both sides, about 4 minutes per side. Remove and cover to keep warm.
Add the onions and cook, stirring, for 3 minutes.
Add the Calvados and cook, stirring, to deglaze the pan. Simmer until reduced by about half.
Add the cider and thyme sprigs, bring to a boil, and cook until reduced by one-third.
Add the apples and cook, stirring, until tender, about 2 minutes.
Return the chicken thighs to the pan, add the cream and return to a boil.
Reduce the heat to a simmer, cover, and cook until chicken is cooked through and sauce is thick enough to coat the back of a spoon, about 25 minutes.
Remove from the heat, remove the thyme sprigs from the pan and discard.
Divide the chicken and sauce among 4 plates, garnish each serving with the crispy bacon and fresh chives, and serve immediately.