In my current game as Poland, I have conquered Constantinople, the holy city for Eastern Orthodoxy. I have founded Protestantism. Byzantium was left with one decent sized city (Nicea) and two tiny ones. There was quite the battle for religion after the real war ended. I had used a prophet to remove their religion from all of their cities. Eventually I see a Byzantine GP wandering into my lands and then hits two of her former cities, turning them back to EO. Luckily for me, I had a very widely followed religion and GP of my own came shortly after. This would happen a few times. They would send one in and then mine would repair the damage. Eventually, after I requested she stop sending her prophets into my lands. She refused, I took Nicea and that was it for Eastern Orthodoxy as her last two cities had little faith production.