From the Death Note franchise comes the two Death Note Rewrite movies. However these movies are generally just recaps of events that happened in the anime through a different perspective and the name is a pun on the show's premise.
The comic book Strangers in Paradise, in Vol. 3 issue #43, presents us with both an actual and a metafictional rewrite: It apparently takes place years later, when Francine and Katchoo are an elderly couple with a daughter named Ashley. Ashley has submitted a novel to a publisher, which turns out to be the story of Strangers in Paradise itself, and the publisher suggests a rewrite to make it flow better. After some minor outrage from Francine and Katchoo, they back the idea of a rewrite to make it more true to the "love story" aspect of their history, and the issue ends with the phrase, "End of Version 1." In the following issues, we see different takes of Francine revealing her first pregnancy, finally resolving in Francine going back to Katchoo, causing the rewrite to morph into a "saving throw" of removing a flash forward plot-thread from the start of volume three of the series where it's revealed that Katchoo and Francine had broken up and not seen each other in years (changed to several months and due to Katchoo being caught in bed with Casey). David's death remains intact however.
Less overt but still a bit of a major sting, was the issue of Katchoo's step-father's death. Terry Moore had stated in the book's letter page that the step-father, who sexually assaulted Katchoo, was long dead when asked about the character's family. But he later opted to have him die during the middle of the series' third volume, with an issue dedicated to Katchoo (who didn't know about it until after he was dead and buried) racing to his grave in order to vandalize it with the word's "Child Molester" burnt into the tombstone.
Garfield: In the original strips, Odie is seen as moving in with, and being owned by, Jon's roommate, Lyman. When Lyman was written out, flashbacks tended to show Jon buying Odie at a pet store.
The first two Calvin and Hobbes strips shows their first meeting, which Bill Watterson felt was important at the time. In later strips, Hobbes implies that he is older than Calvin and has memories of his birth.
This began in T3, Where John says he was 13 years old during the events of T2, when he was meant to be 10 (although the actor was 13).
Which would make Sarah 16 in the first one (at one point in T2, the police say she's 29; it's already hard to believe she's 19 in the first.)
Ironically, in several scripts, Judgment Day happened in 1999.
Rocky Balboa completely ignores the events of Rocky V. In the montage of clips shown from previous films, any footage from Rocky V is notably absent. As well, the brain damage Rocky suffered in Rocky V is completely ignored. This is due to Sylvester Stallone being unhappy withRocky V and creating Rocky Balboa as the "suitable" conclusion to the Rocky saga.
The Broad Strokes of Rocky V did happen, like him being retired from boxing and virtually broke. Stallone provided a Hand Wave in supplementary material that said the head injury wasn't as severe as his doctors initially believed, and he presumably never got a second opinion because Adrien insisted it was time for him to call it a day. Obviously Stallone hated Rocky Vas much as the viewers.
Perhaps the most famous (and best handled) example is Tolkien's rewriting of The Hobbit, where Bilbo obtains a ring that confers invisibility in the Misty Mountains. As The Lord of the Rings reveals this to be the One Ring, Gollum's Back Story could no longer have him offering an Artifact of Attraction as a prize to Bilbo for winning the riddle contest; instead, Gollum would never forgive "Baggins" for stealing his ring. A revised edition of The Hobbit was published, and the prologue to The Lord of the Rings explained the inconsistency: the original version was the story Bilbo maintained (building on the idea that The Hobbit was actually an autobiographical novel by Bilbo himself), but Gandalf eventually learned the true story by persistent questioning.
The author hangs a lampshade by explaining that rumors of Ian Malcolm's death were exaggerated, and he still suffers ill effects.
This does not, however, clarify why one of the surviving main characters was talking about Malcolm's funeral arrangements.
In Gary Brandner's The Howling, the character of Marcia is specifically shot through the eye by a silver bullet and drops dead. In the sequel, Marcia is revealed to be alive after the bullet just grazed her. Her eyes are fine and in human form the only sign of injury is a streak of grey hair. Unfortunately, the silver made it so she could no longer transform properly.
J.T. Edson wrote several novels that were 'expansions' of earlier short stories. These novels usually change substantial details of the earlier stories. Perhaps the most significant of the changes is revealing that Dusty Fog had married much earlier than Edson had previously established.
In the Warrior Cats series, the authors came out with a guide book, Secrets of the Clans, when only the first two series were out. It explained how the Clans formed and said that the warrior code was created by the four founding leaders. In the following years, they came out with more story arcs and special editions and heavily expanded on the world, leading the authors to declare parts of it Canon Discontinuity. Code of the Clans shows that the warrior code formed over time in response to difficult situations rather than being established by the Clan founders. Dawn of the Clans, the fifth series, is about how the Clans formed, and the authors have said to consider the Secrets of the Clans story as an elders' tale.
Red Dwarf underwent continuous rewrites; or to be more precise showed a cavalier disregard to its own backstory when there was a gag to be made. Most notably, the idea in the early seasons that Lister had barely spoken to Kochanski was contradicted in the novels, where they had a brief relationship before she dumped him. Later episodes would follow that version. Another major one is Rimmer's light bee; it went from being Rimmer's remote projection unit to actually being Rimmer.
Not to mention that the light bee originally didn’t exist. The only way for Rimmer to leave Red Dwarf was within the confinement of a “Hologrammic Projection Cage.”
At one point, a TV series was in production that would focus on the nephew of MacGyver, who was an only child in the series.
A very minor and easy-to-miss example is in Black Adder II, where Baldrick says, upon being fired in the episode "Beer", that his family has been in the service of Edmund's since 1532. The first series, The Black Adder, begins in 1485, at which point Baldrick is first introduced to Prince Edmund and, indeed, his family.
Smallville does this with character backgrounds and attributes. It's so blatant that it makes one wonder whether the writers/producers are just too damn lazy to go back and re-watch episodes or look up information on their characters on one of the many, many, many online databases documenting every character, in detail, from the main cast to the most throwaway guest star, or they're hoping viewers have poor recollection of the events and they won't go back and look. Or, Viewers Are Morons. For example:
Chloe's mother: Chloe woke up one morning at age five to find her mother inexplicably gone and her father "trying to make waffles" (Lineage) vs. Chloe, at around eight or nine, comes home to watch her mother get carted off by the Men In White. (Progeny)
Chloe and Smallville: Chloe moved to Smallville (or any rural place, as she though farmer Clark "was Amish") for the first time when she was thirteen (Obscura) vs. Chloe lived in Smallville early enough to have been affected by the meteors, allowing her meteor-mutant-controlling mother to accidentally control her and leave for Chloe's safety. (Progeny)
Lex's Mother: Lex's mother was a redhead, as supported by his genetics (Lex has naturally red hair), Lionel's apparent infatuation with redheads (Lillian, Pamela from Crush, Rachel Dunleavy from Lineage, Martha Kent), show creators' confirmation that Lionel likes redheads, and that she appeared as one in Lexmas, vs. Lex's mother was a brunette and Lex dated women based on her. (Bound)
Clark Leaving Krypton: Clark's parents both sent him off to earth (Memoria) vs. Clark sent himself off to earth via some twist in space and time, and his parents were no where to be seen. (Apocalypse)
Brainiac may have killed Jor-El and Lara right after they placed Kal-El inside the ship.
Shawn Ashmore played a villain in a couple of early seasons, only to show up later as Jimmy Olsen. No, wait, that isn't him!... it's his twin brother. And nobody noticed.
Old TV Serials, such as Undersea Kingdon were notorious for rewriting Cliffhangers. "Oh no, Crash Corrigan collapsed in the certain death room! Oh, wait, they introduced a floor-hole between episodes and had Crash jump through it, and thus he's no longer being showered in sparks."
On Full House, Uncle Jesse goes from being Jesse Cochran to Jesse Katsopolis.
In series 1, the grandparents tell Rory and Lorelai at one of the Friday-night-dinners about Richard's departed mother, Rory's great-grandmother. They clearly talk about her in the past tense, she was a wonderful woman, wish you could have met her, etc. Later on, she appears and causes much entertaining havoc. Clearly the writers were embarrassed at having so thoughtlessly thrown away a great opportunity for family dramatics, and just introduced her (Lorelai the first) without even the grace to lampshade-hang the fact that she was supposed to be dead. There is another trope here whose name I don't know, where an actor re-appears in a different role: When Lorelai the first eventually dies, the actress appears at her funeral in the role of her niece /Richard's cousin Marilyn, continuing the legacy by telling adventurous tales about the demised matriarch. Marilyn appears again in the episode when Richard and Emily renew their vows; the writers must have loved her acting, but wanted to switch roles as matriarch Lorelai probably began to wear everyone out (and her death and ensuing funeral shenanigans complete with Emily's breakdown were just too much writer's gold to pass up).
Jess's parents: when Jess first appears, Luke tells Lorelai that "the prize" that is Jess's father left them 2 years ago, i.e. when Jess was 15. Later on, it is stated that Jess never really knew his father as he left just after Jess was born.
The way that Jess's mother Liz is talked about also changes quite a bit; again, I guess as the writers realised that here was an opportunity to introduce another promising character, they couldn't quite keep portraying her as the horrible screw-up, unreliable and not really caring about her son enough, as no viewers would have taken to her. They managed quite well by twisting her story into that of a hippy-chick who has finally found her way, given up drugs and promiscuity, and getting her life together, but from the way they talk about her when Jess first appears, you'd never know she was such a likeable person. They do well though, by having both Luke and herself mentioning, a lot, how she used to be a screw-up. It's a better integration into the story than just having a supposedly dead character suddenly appear without comment...
Kirk veers between personalities, getting quirkier and quirkier as the series goes on. He seems quite reliable and organised in the first season, when he manages Doosey's market, or checks Lorelai's house for termites. He goes more and more nuts, to create more writing (writer's) fun. He also "can't drink coffee" in one episode, but is seen drinking coffee at Luke's diner all the time, both before and after this. Although that could just have been a temporary non-coffee-drinking quirk, like his one-time juice diet.
In season 2, Emily tells a horrified Lorelai that once on holiday in Thailand with Richard, they spent the entire holiday eating incredibly spicy food and skinny-dipping. However in a much later season, when they are "separated" and Richard lives in the pool house and comes into the main house unannounced, and Emily protests "What if I had been sitting here stark naked?!" Richard replies: "you've never been stark naked! We went skinny-dipping once, and you wore an overcoat!"
Paris's friends Louise and Madeleine are always into boys, but in series 1 they are portrayed as also being studious and A- and B- students respectively, whereas later they get bad grades and are portrayed as always having had bad grades and no interest in studying. Bad girls are more fun to write in that respect, but it makes it weirder that they would be friends with Paris.
And let's not forget, of course, the retroactive modification of poor Dean's character! When he first appears Lane Kim tells Rory how Dean is into very cool, hip, of-the-moment bands and literature, and then when love-rival Jess comes on, they have to dumb poor Dean down and have Rory tell Jess how she basically has to educate Dean on cool music (Jess: "Does he know Bjork?" Rory: "I've played him some stuff"). Even much later, when he and Rory are back together and she then meets Logan, Dean gets the bum end of the stick AGAIN, when Logan can discuss journalism and politics and give Rory detailed and superior opinions on her writing, and the have Dean sit in Doosey's market with her, eating day-old sandwiches for a discount, and comment on her article with "I can't comment on this stuff, I just know that I read it and I liked it!"
Rory changes a lot in later seasons, which can be attributed to being influenced by a wealthy life, snobbish friends and boyfriend and being more engaged in other social and intellectual circles with all the positive and negative consequences that stem from that. It doesn't explain, though, how her 'past' changed as well: early seasons described her childhood as a relatively 'normal' one, and that she was a disciplined kid who liked to read and who'd been largely influenced by her mother's street-smart approach and pop culture. Later seasons described pre-teen Rory as a virtual prodigy with eidetic memory (on one episode, she claimed she'd only need to read an obituary once and she'd remember the person's relatives' names a decade later). Partly plot-justified: early seasons depicted a struggle to work her way up at Chilton and eventually get accepted in the Ivy League, so it was more believable if she was a good student but not an actual genius; later seasons led her to be ridiculously successful at Yale (e.g., editing the daily news despite spending a lot of time partying and dropping out and what not), which could only be remotely possible if she was, in fact, a female Einstein.
Lorelai's general cleverness was also rewritten to contrast with Rory's: in early seasons, Lorelai was quite well-read and street-smart and quite an academic match for Rory despite her lack of Ivy League background, etc., which perfectly depicted her as a role model for Rory who wanted to give her the opportunities she missed out on. Later sessions keep Lorelai as street-smart, but dumb her down academically to contrast with Rory's increasing (and, as mentioned above, unrealistic) portray as a genius. Compare Rory's high-school graduation valedictorian speech with her graduation from Yale later on.
Christopher's role in Rory's life changed according to what the plot dictated. Sometimes he was described as an almost-permanently absent sperm-donor who knew next to nothing about Rory's life, sometimes it was mentioned he talked to her once a week, depending on how sympathetic the writers wanted to portray him, and depending on how much they wanted to contrast him with Luke, or contrast old-Christopher with new-Christopher (especially after his father died and he wanted to be much more involved in Rory's life).
God of War II does this to the first game's continuity. At the end of the first game, the narrator expounds upon Kratos's retaining the throne of the God of War for all time, explicitly showing flash-forwards to WWII and modern counter-terrorist forces as she talks of his presiding over all armed conflict. At the beginning of the second game, Zeus strips Kratos of his mantle of godhood and boots him from Olympus, and Kratos does not regain his godhood by the ending. By the end of the third game, Olympus is completely ruined, so there's no throne for Kratos to reclaim...although the The End... Or Is It? ending of the third game still leaves room for him to possibly return.
The creators have said that the OVA has been replaced by Crisis Core in canon, however, how much of Crisis Core is Revision or Re-Write is arguable. In the original Final Fantasy VII game, we only saw part of the Nibelheim incident, and only from the perspective of Cloud and what he remembered following the experimentation, mako poisoning, mental breakdown/denial, etc., so much of the changes in Crisis Core can be considered Revisions (for example, the fact that Genesis was involved in Nibelheim would seem like a Re-Write, except that Cloud never saw him and Zack never mentioned his appearance to Cloud, so that is likely a Revision).
While most of the changes between Metroid: Zero Mission and the original game it's a remake of can be explained away as simple retcons, there's no ignoring the fact that Kraid and Ridley have gone from human-sized to a two-story Godzilla clone and a giant flying dragon respectively.
Word of God states that they were always intended to be the size they were in Metroid Zero Mission.
This happens when a new developer takes over the Tomb Raider series. Lara's whole background is changed to make her more developed. Legend also implies that all but the first Tomb Raider game never happened.
Then later in Underworld, it's implied that parts of it happened or at least Lara mentions encountering a Doppelgänger before. Also, she is closer to Crystal Dynamics Lara than the original. Go figure.
Harvest Moon 64 and "Harvest Moon Back To Nature" have the same characters but are completely different in other respects. Almost everything is rewritten, from the personalties and backstories to jobs and who's related to who.
This more comes with the territory of the Harvest Moon series blatantly recycling character designs and personalities on a mass level. It's just so blatant in Back to Nature because of the fact that that marked a direct case of copying the entire cast of 64, rather than picking and choosing from the series as a whole as is usually done.
The ending of Star Wars: Rebel Assault deliberately rewrites the ending of A New Hope so that player character Rookie One and his wingman Ru Murleen are the ones who destroy the Death Star, instead of Luke Skywalker. Rookie One fires the missile that travels down the exhaust shaft, and many more fighters are seen to survive the attack (at least seven fighters in Rebel Assault compared to the three fighters from the film).
The third release games may count for this as well. In Generation II, it seems like Pokémon Yellow was canon. It is quite evident that Pokémon Platinum was canon as well. Both of these are third release games.
Or the origin of Repto-Slicer. Originally a creation of Bling-Bling Boy's, Repto-Slicer's origin is completely changed later on: apparently, he is actually an alien lizard from the planet "Razoria". In the episode in which this was shown, it is only quickly touched upon, and then he is left on the planet and never returns.
To elaborate on the abruptness of the revelation, here is the dialogue that leads up to the arrival to Razoria
Darth Vegan: "... And I didn't even know that creatures from Razoria lived on Earth!"