On a five year mission, you rarely were away from a base for all five years. You'd do a leg for a year, stop over at a base, do another leg, stop over at another base. Unless you were a deep space exploration ship, you'd be resupplying every 3-6 months. You'd be able to reload your Photons at any base, and if you weren't going near a base, you could technically pull alongside a freighter that might be near by and grab a dozen or so.