This is what it says in the FAQ:
Q: What happens if one of my players becomes academically ineligible?
A: You'll lose the player for the next semester (he'll still be on the roster and be able to practice, but can't play in games). If his cumulative GPA is still not above 2.0 at the end of the next semester, he'll be academically ineligible for another semester. In addition, each time you lose a player to academics, your reputation will take a hit.
Q: How many academic terms are there per season?
A: There are 2 academic terms per season. You'll receive a mid-term report around game 6, then the final grades will be posted around game 12 for the first term. Around game 18 you'll receive another mid-term report and around game 24 you'll receive final grades for the 2nd term. Cumulative grades will be updated after the final grades are posted for each term.
Not 100% sure how clear that is but I'm guessing you'll get him back after the 24th game? Been a long time since I've had a kid go ineligible in season too tgiugh.