In a large ziploc bag or resealable container, whisk the apple cider, apple cider vinegar, cinnamon, 1.5 tsp. salt and 1 tsp. ground black pepper. It will take a little effort to blend in the cinnamon but it'll get there. Reserve 1/4 cup marinade separately.
Add the chicken thighs to the marinade and toss to coat. If using a bag, squeeze out the air, seal, and then massage and flip around the bag. Let the chicken marinate on the counter for up to an hour or up to overnight in the fridge, turning the chicken halfway through marinating time. Bring to room temperature if it's in the fridge.
Heat the oven to 425 degrees.
Rinse and pat dry the swiss chard (doesn't have to be perfectly dry). Trim off and discard the bottom of the stems. Separate the leaves from the stems and roughly chop both. Add them to a baking sheet.
Peel the sweet potatoes and chop into approx. 1/2 cubes. Peel and chop the shallots. Core and chop the apple. Add these all to the baking sheet. Toss with the oil, 2 tsp. fine sea salt and approx. 1/2 tsp. freshly ground pepper. Just when you think everything is coated, toss an extra 30 seconds to really make sure. Spread out on the baking sheet, aiming for a single layer as much as possible. It might seem like too much but the chard will shrink as it cooks. It's okay if some of the chard leaves stick out.
Remove the chicken from the marinade and place on top of the veggies. Discard the marinade. Gently pat the chicken dry with a paper towel and sprinkle with flaky sea salt and freshly ground black pepper. Bake for 25-32 minutes, depending on their size, until an instant or probe thermometer reads 175 degrees (make sure the thermometer is touching only the meat, not the bone).
Remove from the oven, sprinkle everything with the fresh thyme, if using, and remove the chicken to a plate. Drizzle the reserved marinade over the veggies and gently toss to coat. Serve the veggies with the chicken.