Plenty of people use it incorrectly, and it certainly is annoying. They use it for effect, when it just doesn't work, because they really mean something like "well it was pretty much [this]", which breaks it's own meaning.

Someone near the top said "All but one." This is the right way of using it as a "nearly" meaning, because you are setting up a group and then eliminating almost all of it. Not a sloppy "the civilization was all but destroyed" when they mean it actually got destroyed and there is no remaining item to be "all but" about.

I sometimes use "all but" to mean "there are possibilities but definitely not this one." For instance: "In all but tiny quantities, the poison would definitely kill you." Any quantity you can imagine, that isn't tiny, fits the bill.

So it's a matter of where your focus is intended. You are either eliminating everything except for the last item, or you are separating the bulk away from the item to be eliminated.