The Chaotic Masters has an In-Universe example — the Dazzlings are the only members of the Chaotic Masters' harems whose fates are known, as according to them the other brides all vanished without a trace while trying to meet at a fallback point following the Masters' defeat. The Magic Mirror eventually reveals that they were sealed away some time after their husbands were.
Fantasy of Utter Ridiculousness: This trope is addressed by Yukari. Antagonists that Coop had previously fought with but threatened to resurface at the end, only to never be seen again past their debut episode, were dealt with by her in some way. The last remaining fragment of the REGIS Mk. V, for example, was given to Suika to be crushed within one of her black holes.
Fist of the Moon: Inverted. Most readers completely forget that Mamoru is supposed to be somewhere, as he never appears or is mentioned in the first few chapters. Then he returns in chapter 5, and we discover he was studying abroad in China. So basically, we found out the mouse is okay before we're told it was thrown off-screen.
The Great Starship Battle: None of the plot threads are resolved and we never find out what happens to the surviving characters beyond a vague description of the Doctor's other selves being "destroyed by fire and paradox".
Eleutherophobia: How I Live Now begins with Tom trying to jailbreak a Yeerk phone, but after the main plot with Rachel gets going, it's never mentioned again.
Embers (Vathara): In chapter 51, the flashback/vision to Temul's attempt to warn the Western Air Temple about the upcoming Fire Nation attack, we learn that Gyate (later revealed to be Aang's mother) had a daughter, who was almost old enough to be given to the Eastern Temple to be raised. And that she was pregnant at the time of the attack. The fact that Aang may have relatives out in the world is never touched upon again.
Calvin & Hobbes: The Series: One scene has Calvin and Hobbes attempting to transport their snowmen to safety. Once Calvin's mom brings him a camera, the plotline is abruptly dropped and never referred to again.
A Force of Four: In the beginning, Kara and the JSA wonder why most of supervillains have been gone since the last Crisis. It's revealed in another Dark Mark's Supergirl fanfic — Hellsister Trilogy — that they were forcefully recruited by Darkseid to conquer another Earth.
Kara of Rokyn: Nasthalthia Luthor tells two villains the history of the feud between Lex Luthor and the Kryptonians, introduces both of them to her uncle Lex... and isn't seen again.
There has been no mention of what Sportsmaster has been doing all this time, though it seemed that his reputation was still in shambles after he deserted the Light in season 2.
While Mongul is finally mentioned as having been shot into space in his pod, there's no mention of whether Despero survived War World's destruction. (A mystery that would remain even in the Sequel Series.)
Twice Upon a Time: At one point, Super Improved Cell worries about the fact that one of his components—a Yakumi alien named Ketchup—can telepathically contact her planet for help. The way it's phrased comes across as though it's building up to be a plot point, but nothing ever comes of it and Super Improved Cell is killed several chapters later.
In It Was Written on Their Wrists in the Stars, Egon mentions that he's never babysat anyone before, then later that he has a brother but they're not close. The protagonist is deeply curious as to why those things are truenote even though the babysitting one at least is normal, since considering the timeline, Egon grew up in the '50s and '60s, and back then, boys didn't usually babysit unless the children were their siblings, making it seem like they'll have plot significance, but they're never brought up again.
Bobby's reaction to Lincoln in squirrel suit: Clyde appears to kick Lynn Sr in the leg and knee at the family front door of the house, angry that they drove his own best friend, Lincoln away with the bad luck superstition thanks to Lynn Jr's lies, before running off crying. He is never seen again for the rest of the story and is even unaware that Lincoln comes back to Royal Woods, after being brought in by the Santiagos when he was staying in a New York hotel and eventually forgives his family.
In Singled Out (not to be confused with the episode):
Lincoln keeps having recurring dreams about growing up to be a millionaire comic book writer but in the process drifting apart from his family. However, they have no effect on the plot.
Lola keeps insisting that the "war" she's leading against Lincoln will benefit him in some way, and that by the end of it, he will experience "salvation", but it is never revealed what she means. Later, on, she turns out to be secretly Satan, but this doesn't elaborate on what she means by experiencing salvation.
In A Town Hates a Boy, Lynn drinks some rat poison, but a few scenes later, she's fine. The author would later confirm that she threw up before it could enter her bloodstream, but that isn't mentioned in the story.
Where There's a Will: One of Lori's siblings (it's unclear who) mentions that they've taken Lily's temperature and she seems to be running a fever. They suggest taking her to the pediatrician, but Lori never appears to, yet Lily never seems any worse for wear in later scenes. Perhaps justified, since the story was All Just a Dream.
Inquirius and Cookie Dough (who was a core member of Star Fleet in the first one) don`t play any role in the sequels. According to Word of God that`s because he had no idea how to use them anymore. The same goes for Abra Kadabra, who is only there to make Goldwin come alive.
Another example is My Brave Pony: Star Fleet Magic II one-shot character Cerise, who, despite being a high-ranked Starfleet member and being only the 3rd character shown to be able to use the Uniforce, is only mentioned once in passing later. Averted from VI onwards where she's made a more recurring character... who completely sucks at doing her job so Lightning can save the day.
Celesia's nuclear weapon arsenal is brought up once and then never mentioned again.
The same thing happens with the weapon that only The Chosen Mare can wield. It's the MacGuffin for the first half of the story, and then completely ignored in the second half.
The Vinyl and Octavia Series: In Vinyl and Octavia Machete Their Way Through the Jungle, Vinyl's motivation for going to the jungle and fighting her way through it alongside Octavia is so that she can find an ancient treasure which she thinks can save her dying father. After this story, her father is never mentioned again and it's unrevealed what his fate is.
A Crown of Stars: In chapter 8 Shinji and Asuka run into their counterparts of another universe. After that chapter those counterparts were not seen or mentioned again.
Futures Freak Me Out: Asuka states that she has not seen Misato or Rei in a long time.
The Second Try: After Lilith is destroyed and Gendo shoots himself in the head, it's never revealed what happened with Adam being implanted in his hand. However, when he semi-wakes up from a coma during the last chapter, he notes that he can't feel his right arm. Hmmm...
Thousand Shinji: It's never revealed what happened to the remaining Rei clones after the battle against Armisael. Or the NERV staff who survived the Final Battle.
PnF: Stolen Identity: At the end, Phineas and Ferb leave Ferb's Evil Twin by the lake with the device he had Phineas help him build...yet we don't know where the Evil Twin came from, why he picked Phineas, why he looks like Ferb and why he needed the machine to begin with. Though given the author's style, this isn't as bad as it could be.
Patient Name Propulsion: Lampshaded. Jet mentions that he doesn't know where Sunspot, who was absent from the first story, disappeared too, and Sunspot is indeed never seen or mentioned again from that point on.
Little Hands, Big Attitude: Throughout the entire series, it's never once mentioned what happened to Rachel, Randall and Jojo after the events of Sonic the Hedgehog 2 (2022). Which becomes especially weird when Agent Tower breifly mentions Operation Catfish (how Rachel and Randall met) during a report. Probably justified as they live in a different city, but the fact the Wachowski's visit Tom's parents yet never appear to call Maddie's sister is just odd.
Gensokyo 20XX: This happened to few characters. While some were Put on a Bus, were Killed Off for Real, or, at least has their absence explained by other in-series things, it's not said what happened to Shinmyoumaru, Nitori, Reisin, Kokoro, Rumia, Miko, Tenshi, Ren's siblings, Pug and Mine, Mamizou, Yuuka (besides being implied to be Killed Off for Real), or Flandre, especially when they aren't mentioned in the final chapter of 20XXV.
Lost Soul: Starscream shows up in the second chapter and attacks Bumblebee, only to be punched into stasis by Megatron. Apart from a brief mention later on, Starscream never appears again, and we never learn what happened to him after he entered stasis.
, Egon mentions that he's never babysat anyone before, then later that he has a brother but they're not close. The protagonist is deeply curious as to why those things are truenote , making it seem like they'll have plot significance, but they're never brought up again.