I usually refinish my kayak every 4 years. I sand off all varnish, fill any deep scratches with epoxy, use a fibreglass patch on any breaks, and sand it down real smooth before varnishing. I prefer to do it this way so that any micro-scratches are guaranteed to be filled. This way I know my kayak will always be in top shape even if it is showing many battle scars. I think you would do well to sand off the varnish and fill with epoxy as Bill has suggested.

Robert N Pruden