http://insidemovies.ew.com/2012/02/03/george-lucas-star-wars-digital-yoda-phantom-menace/

GL speaking: "one of the things we did improve was a digital Yoda into the first film, The Phantom Menace. We just couldn't make it work. So we came close, we got Jar-Jar, Sebulba, Watto and a lot of other characters. But we couldn't get Yoda. Which was much harder to do. And so when we did get that accomplished, (as they show the only TPM digital Yoda shot from the theatrical version) which was before the second film. We went back and put the digital Yoda back into the film, as it was originally intended to be.

The Making of Star Wars Episode 1 The Phantom Menace

pg. 96

"Neither Lucas nor McCallum had ever considered attempting to reintroduce the character of Yoda without Frank Oz as the man behind the puppet. "I'd been speaking to Frank about it off and on for two or three years before we did the movie," McCallum said. "There was just no way we were going to do it without him. We fit out schedule around his. He'd just finished a movie, and he fit us in for two days between t he completion of his movie and the start of his press conferences. Two days and he was gone. But it was essential to have him there. Yoda would not be Yoda without Frank Oz."