Yes. The only difference in the top end between 500s and 550s is the bore size, and also potentially a minor modification to the rocker shafts in the cam cover. Completely compatible, however.
The 550 bottom end is a better design, however. The transmission and clutch were reworked by Honda in light of some design flaws in the 500... Might be just as well off to find a whole 550 engine if you haven't put a bunch of money or custom work into your 500 bottom end.