In the last CBA the league had the authority to make teams prove that the player on LTIR was legitimately injured long term. I imagine that will be the same in the new CBA. I would also imagine that periodically the player will have to undergo exams to prove that he is still legitimately injured. They aren't going to let one diagnosis last for 5 seasons without some proof that the player is still injured.
What could in theory screw a team like the Flyers, especially because Pronger's is an over 35 deal and he has a NMC, is if he makes some sort of recovery a year or two down the road that would leave him unable to qualify for LTIR. Yes it's unlikely. But if it happened, Philly would then have like a 39 year old Pronger with concussion issues that hasn't played in 3 years that you couldn't hide on LTIR. That contract is untradeable and he can't be stashed in the minors to get the cap relief. I can't see the Rangers or Penguins for example sitting there and not complaining if the Flyers were using LTIR for cap relief for years if Pronger got healthy enough to be cleared to play.