Depending on which version you're talking about (the movie version or the comic version), there's a couple of reasons it's gone. In X-Men Origins: Wolverine, he was shot in the head with a bullet made of the same material as the metal in his bones. While his healing power was able to repair his brain, it wasn't able to reproduce the memories that were in the damaged part of his brain, causing him to lose most of his memory.
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