The only year he lost was his 2012 season at FU – when he was hurt for most of the season. Was a frosh at UConn in 2011. So he will have played three years – 2011, 2013, and 2014 – and missed almost all of another (2012) due to injury.
Yes, he has to apply for a medical hardship waiver, but given his injury it should be virtually automatic that he gets another year if he wants it and can come up with an academic reason (which is a very low hurdle). I think this waiver can be requested at any time, and he may well have already been granted it.