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About 100 percent of organims that live and have ever lived aren't and won't be ancestors in any way to any new species, even assuming evolution theory is true. Of course the 100 percent is rounded of, but it's a very small number. You can look at a planet and confidently say the law of gravity applies to that planet, you can look at an organism and confidently say the theory of evolution doesn't apply to that organism, or the theory of origin of species through natural selection doesn't apply.
Natural selection shaped that organism before it went extinct, so up until the point the species went extinct natural selection did apply. Do you agree with this or not? How about an analogy, since you brought up gravity. If we launch a satellite and it escapes the pull of earth's gravity, can we say that earth's gravity never applied to that satellite? Of course not. Yes, there are dead ends in the tree of life, but that is missing the point of how we came to those dead ends.
Could you please outline in what areas our understanding of extinction is underdeveloped. Could you give specific examples where we were surprised that extinction occurred, and were unable to explain it? I can't tell if you are saying that our inability to describe extinction is a refutation of the theory of evolution as a whole. Is this what you are getting at?