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The Tommyknockers by Stephen King? It was a novel and later a miniseries. The article for the miniseries mentions the disappearance being a "magic" act.
http://en.wikipedia.org/wiki/The_Tommyknockers
http://en.wikipedia.org/wiki/The_Tommyknockers_(TV_miniseries)
"Hilly Brown constructs a 'magic machine' which he demonstrates at his birthday party. The device makes several inanimate objects disappear and reappear. But when Hilly makes his brother Davey disappear, the boy doesn't come back."

A book someone told me about when I was young. I never read it. A kid makes his brother disappear as a magic trick, but he really does disappear. He reappears years later. Possibly by Stephen King.