The original Suzumiya Haruhi manga, based on the light novels and written before the highly successful anime, was disowned by its publisher. Most records of its existence were erased. They didn't even try to capitalize on the series' newfound immense popularity from 2006 on by bringing it back; instead, another manga by another author was commissioned in order to capitalize on the phenomenon. One possible reason for this is that the first author did some HentaiDoujinshi about the very same series he was drawing, and firing him and disowning his work was the only way the publishers got to manage the affair. Another likely reason is that the artwork for the first manga was terrible. You can see here for yourself.Mikuru's boobs don't even look like boobs.
Referenced in Excel Saga: In the opening to one episode, the production staff of the show confront Rikdo Koshi (the writer of the original manga) and toss down several doujinshi in front of him, causing him significant embarrassment. Those doujinshi are actual ones Koshi wrote before he did Excel Saga. Guess what the plot of that episode is based on?
The Beach Episode of Sailor Moon R seems to have been disowned, not even appearing on the "uncut" English boxset. Their excuse was that Naoko Takeuchi hadn't liked the episode anyway. Then again, who did? Dinosaurs, people...
Mobile Suit Gundam has "Episode 15: Kukurus Doan's Island", which wasn't featured on the US broadcast or DVD boxset at the request of Yoshiyuki Tomino, who felt it wasn't up to the standard of the rest of the series thanks to horrendously Off Model moments. Ironically, some fans would have preferred that they kept "Doan" and instead removed the previous episode "Time, Be Still", which covers the same concept but not as well and also has tortuously slow pacing. The episode is also still present on the Japanese set, released much later.
The Japanese producers of Pokémon seem to like to pretend that "Electric Soldier Porygon" never existed. This is the infamous episode that featured flashing colors, causing over 600 viewers to go to the hospital with seizures. When news broke of the story in Japan, they aired the same clip again, sending even more people to the hospital. It was an extremely embarrassing event that caused massive problems in the anime industry in general, as apparently something like this could have happened at any time in the previous decade due to the use of "strobe light" animation techniques; they just didn't pay it heed until then. It also nearly killed the franchise. Of course, the producers want no reminders of it — and that includes Porygon itself. Note that no major characters in the games use Porygon either (although that may just be because Porygon is supposed to be rare). What's particularly bad about it is that the cause of the seizures wasn't Porygon at all — the real culprit were explosive missiles launched by an antivirus program in cyberspace, which for whatever reason flashed red and blue when they exploded.
Yuki Kaori had an entertaining way of describing her first published manga (a one shot about vampires): "I wrote this story while I was still dumb — I mean young." She laughs at its narmfulness now.
The title of the third chapter of Axis Powers Hetalia (entitled G-R Nonaggression Pact?) might seem strange, as Russia barely shows up (except to break England's cursed chair) and there is no pact depicted. It turns out that the original opening to the webcomic did depict it, and the pages were removed by Hidekaz Himaruya, having not having done the research on Germany and Russia's pre-WWII relationship and the conditions of the Molotov-Ribbentrop Pact. Needless to say, he rectified part of the problem in a later chapter and finally depicted the pact, but once American fandom found the original deleted strips and scanlated them, they would come back to haunt him.
Another set of strips titled "Italy Scribbles" were purged from the site in 2008 for containing sexual content involving France, Spain, and the child version of Italy. Though France and Spain back down before they cross the Moral Event Horizon, their overall behavior in the comic shocked some fans when these strips were also recovered and scanlated.
Strike Witches, despite its current successful anime, light novels, and manga series, had a very rocky start that's been quietly ignored by the writers. For the first manga, "Maidens of the Blue Sky," the artist was originally told to make it a bit ecchi. It was then canceled because it was too ecchi and focused too much on fanservice at the expense of everything else (which, believe it or not, is still true, even compared to the current anime). The second manga, "Maidens in the Sky," wasn't much better. The problem this time was just that it wasn't very good, and contradicted the anime in quite a few ways. Although the actual events in these manga have since been ignored, the characters in them have actually reappeared in newer material.
Robotech: The majority of the surviving voice actors who worked on the show seem to be enjoying their belated fame. Kerrigan Mahan (Sean Phillips and Bron) seems to be an exception to this. He appears to just have selective amnesia concerning the show.
