If a player plays in any game, he uses up that year's eligibility, unless he applies for a medical waiver and it's granted.
Even for a medical waiver, there are stipulations. The team must provide documentation of a season-ending injury, the player must have appeared in fewer than 30% of the team's scheduled games (usually 9 or 10), and he cannot have played in any game past the halfway point of the schedule.
If a player fails to meet all those requirements, the school can appeal and ask for a waiver. And the NCAA seems to have been a little more generous in granting waivers the last few years.