"In Best Wishes, Jessie & James are classed as Team Rocket's Advanced Troops and are the frontline for Team Rocket in Isshu for Giovanni to help Isshu fall to Team Rocket."

I think that since they're the same uniforms, just black, perhaps Giovanni told them of their "new role" and they dyed their uniforms to reflect this.

It honestly sorta seems like something they'd do. And then fail comically and be stuck with their dyed uniforms giving them a sense of importance for the show.