Yo Lemonshine, why do you have to prepare for something that has no effect?
These things aren't mutually exclusive. Player A didn't get 48 minutes because he had rock bottom stamina. Player B didn't get 48 minutes because the lineup didn't account for the substitution patterns of being on the winning side of a garbage time game.
This is the guy (31028459) I had with rock bottom 1 stamina. Here he got subbed out with 3.19 to go and never returned (as any player who gets subbed out due to stamina depletion does). http://www.buzzerbeater.com/match/66015900/reportmatch.as...
I can swear that 9 out of 10 of his 48 minutes were not actually 48+ but he lost seconds at the end of most games, be it a blow out or not. I had to sell my weakest trainee in order to make sure I'd be able to round his minutes, but it still was a nightmare because it was completely unpredictable and I ended under or overplaying other players. In S26 he also averaged 4.2 fouls per game which means in many cases I didn't even get to see how his game would end. I think he managed to foul out in the first half more than once.
Why not just train stamina for a week? It kind of sounds like you cost yourself more than a week's worth of training anyway, in addition to the other complications.