From Wikipedia:
For the 1999 revival, Peter Stone revised the libretto, eliminating what were considered insensitive references to American Indians, including the songs "Colonel Buffalo Bill" and "I'm An Indian Too".[10] Stone said, "The big challenge is taking a book that was wonderfully crafted for its time and make it wonderfully crafted for our time... It was terribly insensitive...to Indians.... But it had to be dealt with in a way that was heartfelt and not obvious... In this case, it was with the permission of the heirs. They're terribly pleased with it."[11] Stone also altered the structure of the musical, beginning it with "There's No Business Like Show Business" and presenting the musical as a "show within a show".[9]