Overcoming prejudice is a classic character growth trope. If a PC takes prejudice as a flaw on their character sheet, it would be suitable to let them develop and work it off during roleplaying. You don't need to be constrained by the game mechanics to maintain a flaw that it makes sense to remove through good gameplay and roleplaying.
If you really need to have a flaw to maintain game balance in terms of character points or something, then you can quite easily develop another, different one to replace the one that you've overcome. Personalities can change over time, so it's reasonable for character quirks and flaws to change.
Luke: Congratulations, Han.
Han: Thanks! It blew up just like I planned!
Luke: I meant on getting married.
Han: Oh, right.
R2-D2: Yeah, let's hope that doesn't blow up.
[SFX]: < eegoo boop poppity >
Wedge: Luke, good buddy!
Luke: Wedge, I need to apologise for how I've been treating you.
Wedge: What? No, you weren't getting too close. I'm good with a bromance.
Luke: I never trusted you, because you were a shapeshifter. But... I was wrong. I'm honoured to work with you.
Wedge: Oh. Well I'm glad you stood by me anyway. That special mission to Rendezvous Point Zeta was a highlight of my career.
Luke: That wasn't really trying to help you, sorry, but I'm glad you turned it around. You're one of our best agents, and I know you're on our side.
Han: As long as he doesn't shapeshift himself a goatee.