How many coats of the clear finish did you use? You should have at least 2 coats for good protection, 3 thin coats is better. The stain shouldn't be removed if there is enough clear finish protecting it.
Suggest a very good cleaning, restain if needed and clear coating with several thin coats.
You could try a tougher clear coat. Use McCloskey's Man-O-War Marine Spar Varnish, very tough and UV resistant when fully cured.