Wally-
Try sanding with 60-80 grit drywall screen or a high quality sandpaper that doesn't easily load up (like 3M). This will likely remove most of the discoloration and you may find that you don't need to replace the rub rail.

We use acetone with scotch brite pads. Then, we apply a protectant, such as ArmorAll. Restores it to a new appearance.

Soft scrub with bleach applied with green scotch pads also works. I follow that with acetone and then apply  protectant. 

[quote=Wally-1840]... has anyone replaced the rubber rub rail while the boat is in the water? If so can you do the side opposite the dock from the deck? ...[/quote]

Sort of.  Last summer I somehow managed to yank a chunk of it out of the metal bracket while maneuvering at a fuel dock (I think it snagged on a splinter on one of the old pilings), leaving a stretched- out 2 foot long loop hanging.  Two of us managed to work it back into the bracket while on a mooring: one hanging over the rail feeding it into the groove and the other in the dingy with a rubber mallet banging it in and compressing the adjoining material in the track.  Not easy, to say the least; I can't imagine trying to do a whole side of the boat this way while in the water (unless you could have it facing a floating dock).

I use my dinghy at the dock to do the non-dock side.  Cleaning and treating as above too.  I have problems with mine stretching out of the track when rubbing pilings or dock walls. Takes a while to work it back in but it gets the job done.  Hanging over the edge for any amount of time for my 65 year old body doesn't work so well.