### Godot version

Godot 4 stable and Godot 3.x LTS

### System information

Fedora linux

### Issue description

If you use some custom logic inside _integrate_forces() to alter the state linear velocity and there is any reference to linear_velocity in physics process, the result in godot 3.5 is that it moves just a little bit, while in godot 4 is totally still.

### Steps to reproduce

For the example i created a simple scene in which i apply a force on the linear velocity in  _integrate_forces()  and added a line that add zero to it in physics process. You will not see any move, but it will work fine if you comment the line adding zero.


### Minimal reproduction project

[PhysicsBugReproduction.zip](https://github.com/godotengine/godot/files/12139772/PhysicsBugReproduction.zip)

const SixDOFJointData *g6dofjd(static_cast<const SixDOFJointData *>(joint_data));
			for (int axis = 0; axis < 3; ++axis) {
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_flag(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_FLAG_ENABLE_LINEAR_LIMIT, g6dofjd->axis_data[axis].linear_limit_enabled);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_LINEAR_UPPER_LIMIT, g6dofjd->axis_data[axis].linear_limit_upper);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_LINEAR_LOWER_LIMIT, g6dofjd->axis_data[axis].linear_limit_lower);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_LINEAR_LIMIT_SOFTNESS, g6dofjd->axis_data[axis].linear_limit_softness);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_flag(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_FLAG_ENABLE_LINEAR_SPRING, g6dofjd->axis_data[axis].linear_spring_enabled);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_LINEAR_SPRING_STIFFNESS, g6dofjd->axis_data[axis].linear_spring_stiffness);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_LINEAR_SPRING_DAMPING, g6dofjd->axis_data[axis].linear_spring_damping);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_LINEAR_SPRING_EQUILIBRIUM_POINT, g6dofjd->axis_data[axis].linear_equilibrium_point);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_LINEAR_RESTITUTION, g6dofjd->axis_data[axis].linear_restitution);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_LINEAR_DAMPING, g6dofjd->axis_data[axis].linear_damping);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_flag(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_FLAG_ENABLE_ANGULAR_LIMIT, g6dofjd->axis_data[axis].angular_limit_enabled);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_UPPER_LIMIT, g6dofjd->axis_data[axis].angular_limit_upper);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_LOWER_LIMIT, g6dofjd->axis_data[axis].angular_limit_lower);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_LIMIT_SOFTNESS, g6dofjd->axis_data[axis].angular_limit_softness);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_RESTITUTION, g6dofjd->axis_data[axis].angular_restitution);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_DAMPING, g6dofjd->axis_data[axis].angular_damping);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_ERP, g6dofjd->axis_data[axis].erp);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_flag(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_FLAG_ENABLE_ANGULAR_SPRING, g6dofjd->axis_data[axis].angular_spring_enabled);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_SPRING_STIFFNESS, g6dofjd->axis_data[axis].angular_spring_stiffness);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_SPRING_DAMPING, g6dofjd->axis_data[axis].angular_spring_damping);
				PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(joint, static_cast<Vector3::Axis>(axis), PhysicsServer3D::G6DOF_JOINT_ANGULAR_SPRING_EQUILIBRIUM_POINT, g6dofjd->axis_data[axis].angular_equilibrium_point);
			}
		} break;
		case JOINT_TYPE_NONE: {
		} break;
	}
}
void PhysicalBone3D::_on_bone_parent_changed() {