Not certain what your desire is
Dan,
One labor intensive suggestion I could make is to test a small area with rubbing compound applied with a small brush and see what color you expose, can't sand it obviously and this method would be an immense job with a toothbrush!
I inherited the coating I use on my deck. When I bought (Dina G) LAYLA II in 2005 she came with a quart of #30 Taupe
http://www.kirbypaint.com/index.php
I would suspect the nonskid profile on your deck is most likely similar to mine and yes it would be a gelcoat masked and initially applied to the deck mold.
The PO obviously was looking for a bit more contrast or perhaps some fading and perhaps as with your situation, got him inspired. First off the paint I have used/ subsequently replenished from George Kirby Paints finishes almost matt, it's a very high solids enamel and I apply it with a brush, brushing it out extensively so it does not fill the texture. Between the nonskid profile of the deck and the paint surface itself it provides a very non-slippery surface. I'm going to say the deck has been painted at 5 year intervals and it pretty much covers in one coat. Since the 31 is a bit of a different style I elected to paint the entire deck and cabintop surfaces this last time out summer before last. The deck is molded in panels and was contrasting between the non-skid color and the framing. I did it all.
I suspect a coating like this tends to age over the entire surface and with oxidation tends to erode off pretty uniformly, ie: not just from the top of the texture. The cockpit floor and bridgedeck I would say have been recoated at perhaps 3 year intervals taking obviously more direct wear.
Last option I guess would be application of a complete new non-skid surface, and provides an altogether different appeance and texture.