Well they could take a few steps to prevent upper-atmosphere lightning as well. I mean, they can't stop it from hitting the shuttle by they can keep working with the tiles to stop them from cracking and stuff. You can't ignore a possible problem just because it's harder to resolve.
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A man once asked the Buddha, "How does one escape the heat of the summer sun?"
And the Buddha replied, "Why not try crawling into the blazing furnace?"