It would be a tough decision indeed for the team managers. Displacing one or more players will always be difficult to do, especially if the player/s involved have been with the program since its inception.
It was easier back then with the NCC team. Danding Cojuangco had full grip with the country's basketball program and no one was capable of questioning him - not even BAP President Lito Puyat who could only lick his wounds for being a paper president. When certain players were removed from the program whether voluntarily or otherwise, (Ricardo Brown, Willie Pearson, Ricky Relosa, JV Yango, Frankie Lim, John Copada, Teddy Alfarero, Louie Brill, etc), or was dropped from the final roster (Naning Valenciano, Bong Ramos, Jun Tan, Jong Uichico) to give way to the naturalized players, no one complained. Or at least, no one knew that they were complaining. I think it was because Cojuangco was still paying for their salaries, and since Jacobs needed practice players to simulate the opposing team's players, the team normally had more than 12 players in its roster. And when the final reckoning is done by Coach Ron Jacobs, it was clearly understood among everyone that this decision was done for the best interest of everyone.
Of course, so long as the other players that will be dropped will still be receiving salaries even if they are dropped from the final 12-man roster, and granting that proper counseling will be given (or has been given) to them in case they're not taken in, then it shouldn't be a problem.