Let me give an example so i can better understand.
Lets say I hold pen in my hand and hold it up and keep it stationary. Newton's third law operates. :gravity force = reaction force of my hand
Now lets say I raise my hand. What happens to Newton’s Third law now that we have second law operating?
No! That is not Newton's third law. Newton's third law says the gravitational forcing pulling down on the pen by the Earth is equal to the gravitational force pulling the Earth up to the pen by the pen. Also, the reaction force of your hand on the pen equal to the reaction force of the pen on your hand. Newton's third law does not assert equality of the the reaction and gravitational forces. For that, look at Newton's first law instead.