Don't do anything yet. Be SURE they are scales and not just the skin itself, or scale scars as Pat put it. If it was done by an experienced bowyer, I'm betting all the scales have been removed and it's just a 'coarse' set of skins.
Additionally, it was probably finished after the skin application and if you put an uncompatible finish over top of it, you may end up with even worse problems. If your finish doesn't adhere well to the current finish it may crack and flake off, then you may end up stripping the skins off and starting over.
I've put on rough skins, and even after every single scale was removed and finish was applied, they were still rough and would feel very 'catchy' when rubbed against the grain. Heck, one of them feels like the rough side of a farrier's rasp :^) I was even concerned for the durability of the string loops due to stringing and unstringing.
One thing that helped a little bit was to burnish and sand a wee bit with the grain of the skins between coats of finish. You have to be careful though because it's easy to damage the skin, especially the tips or points of the scars.
In your case, I would start by contacting the person who did it for you and ask them if they removed every scale, and what they used to seal it. Who knows, in the end, you may be better off just leaving it alone.