Did I Mess Up My Build?

I think I might have screwed up. This is my first time ever playing this game. I just finished chapter 4. But due to a misunderstanding of how the P Organ upgrade system works, I used 4 quartz on 4 separate abilities in phase 1. I didn't realize that I should have used the 4 quartz on two abilities in order to unlock phase 2. It sure looks like you can't respec the P Organ. It's still early in the game, so if I did goof up, starting over wouldn't be that big of a deal. What do you recommend, please?