However, to start things off for the second half of this list, we have another reason why a portion could go "missing" for English release: It was originally released via video game!
Debuting back in 2001 in the pages of Monthly Shonen Jump, Dragon Drive by Ken-ichi Sakura told the story of kids who are into the titular VR game where they fight alongside mystical dragons... only for the game to actually have a connection to an actual fantasy world, Rikyu, where said dragons come from. The manga itself wound up being split into two halves, with the first starring Reiji Oozora as he & some friends (& enemies) find themselves in Rikyu, while the second starred Takumi, the little brother of Makino (one of Reiji's supporting cast), & sees the Earth ruined when the dragons of Rikyu come to the players' world. Though the manga itself would run until 2006 across 14 volumes (split roughly evenly across both storylines), it was seemingly meant to be a media mix from the start, as the companies Bandai, Chan's, & Org were credited as "In Collaboration With" below Sakura, so it's no surprise that there were video games & even a collectible card game based on Dragon Drive, as well a TV anime adaptation by Madhouse that ran between 2002 & 2003 for 38 episodes. While Viz would eventually release the manga in English from 2007 to 2009, though it never received a digital re-release (so it's not in the SJ Vault today), Bandai Entertainment was actually first to bring the series over via the anime, releasing all 38 episodes across 10 dual-audio DVDs in 2004 & 2005, followed by two boxsets in 2006. I actually included the Dragon Drive anime in the 2016 license rescue list, as some of the DVD singles & boxsets have since gotten rather expensive, especially the second boxset.
However, back then I had no idea that Bandai Entertainment's releases were technically "missing" something... an entire episode, in fact! That being said, though, it's not like Bandai Entertainment willingly skipped over it, and in fact the people there may not have even known of this episode's existence, since (to my knowledge) it was only ever released once, and as part of a video game release. As I mentioned before, Dragon Drive had some video game adaptations, three to be in fact, but we'll be focusing on the final, GameCube game, Dragon Drive: D-Masters Shot, a 3D aerial combat/rail shooter developed by Treasure! Released on August 8, 2003, D-Masters Shot came out roughly five months after the TV anime had finished airing in Japan, so it was decided that the game would actually include two GameCube mini-discs. The first was the "Game Disc", which contained the game itself, but the second was the "Anime Disc", which contained an episode-length OVA, Shinku no Himitsu/The Secret of Evolution, which was effectively Episode 39 of the TV anime & acted as an epilogue to the show! Now, to be fair, it's not like the TV anime had an unfulfilling finale or anything like that, but when I realized only a few years ago that this (mostly forgotten, despite the developer) GameCube-exclusive video game contained a bonus epilogue episode for Dragon Drive, one of those early anime I watched when I first started getting into the medium in the mid-00s, my mind was absolutely blown away.