Does anyone know if an injured prospect gets the losses back? Or makes up for the lost time? If he improves five points in his first year, then improves only a point the second year due to injury- will he then be "x" short of projections? Where is the expected development in the second season minus his actual development? Will another owners projected ratings reflect this change, if there is one?

there are lots of variables.  so many that it is impossible to give or know a definative answer.  But I can tell you that medical and training budget is huge in determining how badly a player is affected by an injury.  Getting them both up to 20 ASAP is generally acknowledged as smart.  AFAIK a player cant really get the lost time back, but makeup will help a player rebound as well.  Ofcourse the age of the player will enter into it as well.