Confirmed that you keep the highest bonus of your aircraft. I used a carpet plane as a test subject, and as you see, I changed the livery to copper, which has no bonus of its own. I hope this is a temporary fix, as it isn't the ideal solution. It limits GI itself from coming up with alternate bonuses (lower fuel consumption, etc.), as you can't alter the bonus to a different one. It's good for now, but detaching the bonus from the livery by making them both floating entities will be the ideal solution imo.