To clarify things a bit. There is only one instance of each persistent symbol per document. So if a persistent symbol is on two different scenes we simply move it from one scene to the next after the scene transition.
If the persistent symbol is only on 1 of the 2 scenes involved in the transition it will animate with the rest of the elements in the scene.
If you want the symbol to always be a part of the scene during the transition it is best to use a Standard Symbol.