My advice would be: They took those flaws for a reason. And you can't really turn them into something they didn't have in mind.
Errr yes, yes you can. If someone takes some NQ for the roleplaying aspects, and will pro-actively utilise them in-game, all good.
But it really burns me up when people take '
manageable' flaws just for the BP, and those PC's suddently find their flaws aren't as manageable as they thought they were
-
PC: But my Enemy is on the other side of the world and has no contacts here! And I'm Erased!
-
GM: Enemies have long memories chummer, and they scraped together the cash for a PI to find you, a Sub-orbital to get here and a crew to hunt you down. Now, about your upcoming mission....
-
PCBut, I'm only allergic to Fresh Amazonian orchids!
-
GM:Well, guess what the Johnson wants you to acquire...from a florist...
-
PC: But I took Day-Job so I'd have a steady income!
-
GM: Yeah, but the Stuffer Shack burned down on your shift and you've been fired. Choose from Bad Reputation, Hung out to Dry, Criminal Sin etc etc
This is the same as Initiates choosing the Astral Quest ordeal, and then deciding what NQ they get... falls under my GM Approval category... and those who are reasonable are rewarded. Those who try to abuse the system, get abused.
Many, many players try to abuse the PQ/NQ system, and as such they fully deserve to have their flaws respecced.