Preheat oven to 425°. In a large bowl, combine oil, soy sauce, dijon, honey, brown sugar, garlic, thyme, and red pepper flakes. Season with salt and pepper. Add chicken thighs and toss to combine. Let marinate for at least 30 minutes.
Remove chicken from marinade and place on a large baking sheet lined with foil. Discard leftover marinade. Bake until golden and internal temperature reaches 165°, about 20-25 minutes. If desired, broil for additional 5 minutes.
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