If a player's development is due to experience, the effects that his manager and coaching staff have had on him and on exposure to a higher/lower level of football, it would stand to reason that within your two alternate universes (or two saved games) his rate of development and his appeal to other clubs would differ.
Perhaps, for example, his stats differ because he has two different managers or different coaches in those two saves, who have their own tactical ideas and have emphasised different areas of training. Alternatively, perhaps the game is coded with an element of chance as to how much and how quickly players in other teams improve.
Either way, I would just evaluate him separately, within the context of each saved game, and try to decide whether he would be an improvement to your existing squad.