I think they just wrote it off. Poor Jigglypuff ._.
From The Song of Jigglypuff through the end of the Johto series, a wild Jigglypuff followed Ash Ketchum's group, intent on performing its trademark song without causing its audience to fall asleep. It rarely if ever succeeded. Anything that fell asleep after hearing the song, that Jigglypuff would scribble all over the sleepers' faces. After Johto, Jigglypuff suddenly stopped appearing, but it did feature in one early Advanced Generation episode.
Information found at Bulbapedia.