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Theodore Deland's “Sphinx Card Trick,” 1909, may be the first example of this effect. The earliest ad for it seems to be by W. D. Leroy and appears in The Sphinx, Vol. 8 No. 5, July 1909, p. 97. Ellis Stanyon advertised it in Magic, Vol. 9 No. 12, Sep. 1909, p. 91. In both ads, it is clearly stated to be DeLand's trick. Curiously, you can find a brief description of it in Karl Fulves's Ellis Stanyon's Best Card Tricks, 1999, p. 132. Three cards were placed in a hat and one removed and put into the deck. When the hat was next checked, it contained the one card seen removed, and the other two were found in the deck. Misprinted gaffs were used. A variant, “The Renovated Sphinx Card Trick,” was contributed by Eddie Clever to The Jinx, No. 9, June 1935, p. 34.
The first non-gimmicked method seems to be by Karl Fulves; see “Four Gone,” in his Notes from Underground, 1973, p. 53.