If you change your Neopet's colour or species any paint brush clothing items that your Neopet had previously will be returned to your closet. This means that if you use a paint brush, morphing potion or even the Lab Ray you will keep any clothes that you had earned from your pet's previous colour!
Remember, if your Neopet was a robot and zaps into a new colour, you will need to remove the robot casing clothing items!