This seems to have potential to be a problem. It happened to me this season in one of my worlds with a minor league "roster filler" type player, but it it was a true prospect, I would have been ******.
Minor leaguer suffers a major injury and goes on the 60-day DL that will carry him through the rest of the season and into rollover. After the season is over, I cannot promote him to the next level because he's on the DL. Rollover happens. He retires because he wasn't promoted.
Something should be put in place that will either (a) allow you to promote a guy on the DL; or (b) not allow players to retire if they went into rollover on the DL.