So your argument is that something might, in some extremely rare cases, go wrong, and that is why you'd rather do it the manual way? That's basically like a carpenter refusing to use power tools, because they might, theoretically, explode.
To quote myself, "fix a single file manually, instead of a dozen or a hundred or a thousand".
And what happens when you need to rename, say, a method name that's also used as a variable name in many places? xWhat happens if multiple classes define the same method name, but you only want to rename that method for a single class?
Yes, you can probably do it in sed. If you're used to it enough, you can probably do it pretty quick, with sufficient regexps that you only have to debug a few times.
Or you can right click or hit CMD-. or hit F2 or whatever with your cursor on a method name, type in the new name, wait 2 seconds, and you're done.
Are you relying on a correct and comprehensive project/workspace setup within the IDE?