In the case of Tiny Toon Adventures, some of the retakes wound up disappearing as soon as the show left Fox. When the show debuted on Nickelodeon in 1995, not only did a surprise "new" episode make its debut with no announcement ("Toons From The Crypt," which Fox had banned) but strange differences started popping up, like "Best 'O Plucky Duck Day" having different title cards. "K-Acme TV" now contained a still shot of Elmyra where a video screen with Buster's Easter question once appeared. The retakes had vanished, and have never been seen again on any other network.
Nowhere are the differences more stark than in "Looniversity Daze," a first-season episode that sported a few retakes by Jon McClenahan, who was at the time working for Kennedy Cartoons. This is an odd appearance since "Looniversity Daze" was not a Kennedy production. The regular animation used in the episode is rather ugly, and wherever McClenahan spices it up, it is a vast improvement -- making this loss rather tragic, especially in the case of Buster's hilarious "Dat's my name, don't wear it out" (see video).
The loss of the retakes also creates a sound error in the episode. Hamton used to shake Buster and slap him in the face during "The Learning Principal," and in the DVD version, Hamton stands still while the sounds are heard.
It is unknown why the retakes were lost after 1995, nor where they might currently be stored, if anywhere.