Ive not yet taken the head off but would think if all the head bolts are the same size then its upto you whether you refit the lifting eyes or not, if the head bolts are longer where they mount the eyes and you dont fit the lifting eye then when you torque down the bolts they might bottom out and whilst being at the correct torque they might not be applying the right pressure if any on the head.
Cant remember if either the lifting eyes are held on with the head bolts tho.