a bad r/r will only harm the battery if the bike is running, usually it will just stop running or it will start popping fuses though. From what i have read usually the r/r and stator go out together for some reason. This was not the case for my bike, the stator was fine the r/r just croaked, if it all looked ok then it should be fine, when they go bad they have very obvious visual clues because the wires will burn up and so will the plug.