I just cooked a half dozen chicken thighs this week using the recipe in the Traeger book and they came out really good. very moist. I would prefer a little more smoke so will be tweeking the next batch. The Traeger recipe had the temp set at 350F and cooked for 40-45 minutes, Skin side down and pull at 170F internal temp. Don't turn the chicken.
However there are a number of variables to take into account.
Bone in or Boneless. For boneless they recommend only 30 minutes
BBQ sauce. If you are cooking the whole time at a high temp like 350, then you probably only want your BBQ sauce on the last 15 minutes. As mentioned by others the bbq sauce will char easily because of the sugar. Keep in mind, BBQ sauce is not a marinade. Try marinating the thighs for a couple hours in Zesty Italian Dressing, then apply your BBQ sauce the last 20 minutes of your cooking time.
Size of thighs. Here in Northern California one of the main brands of chicken is Foster Farms. I don't like to use these because the pieces are really small and easy to over cook. I like the ones called Rocky Range which are not quite Organic but from what I call "Scratching About" chickens. The thighs are much larger and obviously that will affect cooking time.
Traeger Temperature- This is one of the more critical items. You really need to know the temperature profile of your Traeger. The newer machines have a digital controller and it varies the auger on and off time to control temperature. I still find that the swings are probably plus minus 25 degrees from the setpoint. Initially I had even greater temp variation and so I took out the grill, drip pan and heat spreader just so I could watch the Traeger operate. What I found was that there was a slight slope on my patio for rain drainage and that as the pellets dropped into the firepot, they rolled to the side opposite the heat element. So the pellets wouldn't start burning until there were pellets next to the heat element and then all of them would burn causing a large overtemp condition. Solution was to turn the Traeger 180 degrees so that pellets fell immediately against the heat element.
Temperature Monitor. How are you monitoring your temperature? Do you have a Dial gauge in the top lid of your unit?
In Summary, you do need to cook chicken by its internal temperature. Biting into a piece of chicken that is not done (red or pink in the center) pretty much ends the meal or causes one to put it all in the Microwave (UGH!!) to finish the cooking. Be careful about high temps and BBQ sauce too early in the cooking process. Know what temperature you are actually cooking at. Personally I would leave the skin on as it helps retain moisture and releases fat. If you want BBQ sauce on the chicken with no skin then remove the skin and apply BBQ sauce the last 20 minutes.
OK, I am getting a bit wordy. Hopefully one or two points will help with your next smoke.