I use a two part filler like builders bog available from buntings and other stores but there are others you can use. You just need to clean the area and make sure it's dry before applying the filler. Unfortunately if you don't want the Cliffy protector to reshape itself into the worn grove you have to do this. These protectors are very thin so that that they sit completely flat and don't disturb the flow of the ball. If you don't fill the worn area, after a while with the ball running over the protector it will deflect.
If you haven't done it before filling the worn area is not as difficult as it might sound. Just mix up a small amount of filler as per the products instructions and apply. The trick is to not use to much at the one time, its best to fill it in two or three goes and not all at once. Try to also avoid putting filler on areas which don't need to be filled or clean it off those areas before it drys. The more you apply the more you have to sand. Just use small piece of fine sand paper and carefully sand, avoiding the areas outside the line of where the Cliffy will cover.