In a large pot, cook bacon over medium heat until browned and crisp, about 3 minutes. Transfer bacon with a slotted spoon to a piece of paper towel to drain. Discard all but 2 tsp of fat from pan. Add half of the chicken and brown well, about 2 minutes per side. Remove to a plate and repeat with remaining thighs.

Reduce heat to medium-low and add onions to pan. Cook, scraping up browned bits at bottom of pan, until onions are browned and beginning to soften, about 4 minutes. Add apple juice, apples, mustard, vinegar, thyme, salt, pepper and reserved bacon and chicken thighs to pan. Cover, reduce heat to low and simmer gently, stirring occasionally, until chicken is no longer pink in center, 20 to 25 minutes.

In a small bowl, stir cornstarch together with 2 tsp water; stir into sauce. Cook until sauce thickens, about 1 minute.