My understanding is that in modern lens design, parallel light that enters the lens assembly will converge and diverge several times. If the damage is on the layer that rays converge, it will show on the final image. If the area is anywhere else, it can contribute to flair or loss of image quality such as sharpness to varying degrees. In other words, it depends on degree and the location of the fault. Since the lens is at the manufacturer for repair, why don't inquire the person who is working on your lens??