This happens with other aircraft that have a working paint folder just called texture, once you call up that aircraft it always overwrites any other paint choice for that model. I usually just make a duplicate of the texture folder, rename it to texture.(reg of the aircraft or similar) and change the configuration to call that new folder in lieu of the basic texture.
You can do the same without keeping the texture folder in place, but if it's a model with a lot of paints then you will have to go through each texture.something folder and rework the texture.cfg to point to the new folder name.