If you develop genu valgum and collapsed arches from low vita d but then levels normalize are the bone effects from muscle weakness permanent?

Maybe: If you have collapsed arches, many times from posterior tibialis stretching or tear, or hereditary flat foot, it generally puts a stress on the knees that thrust your knees into a valgus or "knocked knee" direction. It would be unusual, if it's you, at 25, to have skeletal deformities per se. It iis common when treated with custom molded orthotics to help destress the knees and improve alignment.