There is the material nature and the spiritual nature. The material nature does not disappear when taken over by the spiritual nature. One still has a material nature, but there is a war between them. Once (the material) has ruled, but now the spiritual has control. The material will not give in without a fight.
In the old west a cowboy would break the horse's wild nature to a controlled nature by introducing another peaceful nature to the horse. I cannot psychoanalyze a horse's thoughts. There is a free nature and a controlled nature be it man or eviroment. Is there a question to "once free always free, If a horse has free will does man"?
It s written in the (KJV) "man cannot serve two master". Therefore he has free will. Paul