I'd cover it with a piece of Eternabond roofing tape. You can pick up kits at almost any RV service place but it's expensive when you buy it that way. I buy mine from
http://bestmaterials.com/roof_repair.aspx and keep a whole roll handy. On my living room slide roof it appeared that the line of screw heads close to the outside panel were wearing through the roofing material so I put three strips of Eternabond the full length of the slide roof, overlapping each strip about 1/2 inch. I also fixed a couple of "scuffs" on my roof the same way with just one short strip. Incidentally, I also placed a strip on the roof where the antenna end rests on the roof just to keep from wearing a spot in the roofing.
Be sure when you go to put the strips on the roof that you clean the area well with just plain rubbing alcohol. Make sure your strip is cut the length you want it and when you get ready to put it down realize that when you stick it down, it sticks! You can't move it!
Orv