In order to get different looking bulletholes to appear at the same location, you need multiple textures with the same name. This upload contains up to six different textures for each stock bullet holes. Thus for different flying sessions, there will be different-looking damage to an aircraft.
There is scope for you to set up more folders along the same lines, and create even more variability - there are 16 stock bullet holes, so you could have up to 15 folders.