Many parts of the body are replaced several times in a life time and the skeleton is one of those parts. Bone is renewed by one component that breaks down bone and another that builds bone and both are usually balanced for most of life. Osteoporosis is an example of the bone building/ breakdown getting out of balance in a similar way that astronaut bones get thinner.
This is a challenge that we will have to deal with if we want to extend the range of manned exploration. There are many challenges, dealing with cosmic radiation, long term food supplies and good air are but a few. There are spin off effects to these kinds of studies that more than pay back the cost of the studies.