auto skel_clone = my_skeleton->clone();

// includes and code

namespace {
    dart::dynamics::SkeletonPtr global_robot;
}

void load_global_robot() {
// code to load/create the global skeleton
}

void add_damage(const dart::dynamics::SkeletonPtr& skel){
    std::string leg_bd_name = "my_damaged_body_name";
    auto bd = skel->getBodyNode(leg_bd_name);
    // set half the mass
    bd->setMass(bd->getMass() / 2.0);
    auto nodes = bd->getShapeNodes();

    for (auto node : nodes) {
        Eigen::Vector3d tr = node->getRelativeTranslation();
        tr(1) = tr(1) / 2.0;
        node->setRelativeTranslation(tr);
        // here's the problem -- the pointers 's' are always the same
        auto s = node->getShape();
        if (s->getType() == "BoxShape") {
            auto b = (dart::dynamics::BoxShape*)s.get();
            Eigen::Vector3d size = b->getSize();
            size(2) = size(2) / 2.0;
            b->setSize(size);
        }
        else if (s->getType() == "CylinderShape") {
            auto b = (dart::dynamics::CylinderShape*)s.get();
            b->setHeight(b->getHeight() / 2.0);
        }
    }
}

int main(int argc, char** argv)
{
    auto my_new_skel = global::global_robot->clone();
    add_damage(my_new_skel);
    // if now we print the change shapes (in our case, lengths or size) for the global::global_robot, they will have the changed values and not the original values as they should
    return 0;
}