I don't know that anyone really knows, other than the nhlpa/player/team.
Rarely do you hear any details about why a player is in the program unless they offer up an explanation themselves, because it's generally treated with confidentiallity. Players go into the program for personal issues (addiction, depression, etc) and not PEDs.
I'm sure things like youre asking about are determined on a case by case basis, between the player, league, nhlpa, team, treatment providers, etc. There's not really one defined path you can take when dealing with this sort of thing. I'm guessing PED testing could continue as normal. As for other substances/drugs... who knows.