What if it was only 2? What if they were both NT centers? Should the discount still apply?
I say yes, but don't forget that in my system you only get a discount if their salary this season is higher than last season, so if their salary in season 15 is $300,000 and in season 14 it was $300,000 they get a massive discount of...nothing.
You've conveniently forgotten in your system that salaries are adjusted every off-season against those of the highest-skilled players in the game. It's quite possible to train a player and have his salary decrease (i.e., training a, say, 26yo 300k center from atrocious OD to inept OD).
Another issue that occurs to me (and perhaps I'm not understanding your meaning perfectly here) is that this player got a discount in season 14. If he has the same salary in season 15, and you remove the discount, suddenly he costs more in season 15 than he did in season 14 as a penalty for not increasing his salary, which (excuse me for saying so) is freaking ludicrous.