I was a bit confused on “basically a new car” please look into lemon laws. A brand new car should not have internal engine issues. Lemon laws typically have a three strike and done red line. Furthermore a flashing check engine light indicates engine damage can/ is occurring. Keep careful notes about your dealing and phone calls with the dealership. So far it seems the dealer doesn’t know what the problem is and is blowing smoke up your a**. If the check engine light returns or is on/ flashing take it back for repairs.

Study the lemon law!

Question… was the car brand new or did it have a few thousand miles when purchased?? A cylinder misfire is a serious problem that can cause other problems too, including catalyst failure, extreme poor fuel mileage, cylinder damage. Seems to me this vehicle is a candidate for a lemon law buy back. This is your goal. Keep bringing it back to the dealer for the same complaint and then request the manufacturer buy it back because it’s a lemon. Go ahead and drive the car as instructed.