What red squares?
The pearls vanish when being used, but there is an unlimited amount pearls that you can farm in the dungeon, so it's only a question of personal preference what you skill first, and how much you want to grind.
Viewing post in New Skilltree for the Adventurrers
When I go into the adventurers skilltree some of the ability squares are red others are blue. I tried to inclease the defence stat for all four characters but Ryens square was red and did not increase the others squares were blue and did increase. I don't mind the grinding too much but didn't want to waste time and pearls.