I have precisely the same problem on my '08 Rio M.
If you can, save any of the chunks/chips of EVA material that are cut out/damaged.
If you get some good foot pad glue or some marine grade contact cement,
you can glue the "chips" back into where they came from and glue the chips that
are still attached back in place.
It's unfortunate that the designers chose to "wrap" the EVA all the way down over
the rails as this makes it very easy for the soft EVA to get damaged.
My choice would have been to bring the EVA to the top of the radius of the rail and
then taper it off so that the rail is a double wrap of composite with paint over it.
That's not what they did, and we now have reall problems keeping our Rios looking
Hope this helps,