All Dogs Go to Heaven (Partially Found Deleted Scenes of Animated Film; 1989)
All Dogs Go To Heaven is a 1989 animated film directed and produced by Don Bluth. While it didn't do well critically due to being released on the same day as The Little Mermaid as well as generally being reviewed poorly due to its writing and being overly dark for a children's film, it did very well on home media releases, inspired several sequels, and is regarded as a cult classic.
In the initial test screenings, there were multiple scenes and pieces of dialogue that were ultimately cut from the final film, mostly due to said scenes and dialogue being deemed too dark or intense for a children's film. Two known scenes that were cut include the main character, Charlie, being hit by a car (of which only the aftermath is shown in the official release) and a longer sequence of Charlie's nightmare of Hell. As for dialogue, most of the material that was cut had minor cursing. However, during the song "Let Me Be Surprised", one moment of cursing was partially left in by accident, as Charlie is clearly animated to say "Damn that Carface, I'll kill 'im!", but he doesn't say the swear. The "damn" was still present in the vinyl soundtrack, however.
Theft and Destruction of Full Cuts
Don Bluth reportedly owned a full cut of the film on 35mm film and had plans to get Goldcrest Films, one of the film's production companies, to release a director's cut in the mid-1990s after returning from Ireland. Unfortunately, the print was apparently stolen from him despite being locked up in a storage room. The fate of this particular copy is unknown, though it's likely either been damaged, destroyed, or thrown away at this point.
As for Goldcrest Films themselves possibly having copies, they did not save any of the original art and, according to co-director and producer Gary Goldman, most of the cells and backgrounds "were destroyed or taken to the dump in the UK" due to storing them in optimal conditions costing too much. 
Despite seemingly all uncut versions of the film being thrown away or destroyed, one of the cut scenes has, in fact, surfaced.
During summer 2016, Tumblr user "SteamRunner" went to summer art program. One of Bluth's studio's animators happened to teach animation at said program, where she actually showed the entire uncut hell nightmare scene. One of her friends happened to find the whole scene (albiet without a score) in an archive and, in turn, burned it onto three disks (one for Bluth, one for the animator, and one for himself). She then decided to show her class the scene, at which point SteamRunner recorded it with her phone and finally uploaded the video to Tumblr on June 23rd.
The discovery of this scene implies that there are either some full cuts of the film left or that individual scenes were archived, both of which would mean that the lost scenes can still be found in some capacity.