I don't know about mud flaps, but I used basic paint pens, which can be found at any craft store, to fill in the lettering/logo on the 4Runners trailer receiver cover. It's been a year now, still looks as good as the day I painted it. I chose a silver color that nearly matches the 4Runner's body color. No one has ever noticed it, to my knowledge, but it's still something that I notice.
Maybe something like that will work for ya?