Medical hardship applies to the injured player not the player replacing the injured player. So, if you put a player on R/S and later that season pull it off, then he has used his R/S eligibility for his career (unless he himself later qualifies for a medical hardship).
The criteria to qualify for a medical hardship are nearly impossible to meet. Many seasons ago, I had a player earn a medical redshirt because he was injured in the 4th or 5th game of the season and he did not recover until after the season had ended. That is what it takes to qualify. His health rating went down to a 1.