There's a funny accustats tape where two guys are playing in a 1p tournament, and someone nudges a ball with his stroke. His opponent cries foul, but he doesn't see it that way. In fact I don't think he even tried to move it back. So the opponent's response is to get down, swing, and then casually sweep his stick sideways after the stroke, raking all the balls in front of his hole
I think replace when possible, and if your shot affects the outcome, you owe a ball. I'm not sure what to do if someone moves balls and nobody can tell where they used to be... give up that game and rerack? Take a wild guess? Spot'em?