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Faltings' almost purity theorem. The proof given, for the smooth case, in $p$-adic Hodge theory has some problems, and the proof of the general case in the Asterisque paper Almost Étale Extensions is completely unreadable (at least to me) and also contains some mistakes. We now finally have a very good proof (by Peter Scholze), but the almost purity theorem has been used as a black box for years.
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