Has a movie from a movie series ever been removed/retconned due to fan/general outcry?

Highlander 2

The 1991 theatrical release changed the backstory of the characters from being immortals of unknown origin to aliens from another planet. It was so poorly reviewed that in 1995 they reedited the movie for the 'Renegade Version' and completely removed any reference to them being aliens, along with other improvements.

The Star Wars Holiday Special (1978) would probably qualify.

Once broadcast it's generally been treated as the "Star Wars pariah" and ignored/dsmissed by those involved. Certain parts have been retconned into canon but the whole thing is something that the Star Wars "Powers-That-Be" would have us forget.

The Star Wars Holiday Special is a 1978 American musical science fiction television film set in the Star Wars galaxy. It stars the first film's main cast while introducing the character Boba Fett, who would appear in later films. It is one of the first official Star Wars spin-offs and was directed by Steve Binder.

^Wikipedia

The special is notorious for its extremely negative reception and has never been rebroadcast or officially released on home video. It has therefore become something of a cultural legend, because of the "underground" quality of its existence. It has been viewed and distributed in off-air recordings made from its original telecast by fans, which were later adapted to content-sharing websites via the Internet and bootleg copies.

Since The Star Wars Holiday Special was broadcast, it has received an extreme amount of criticism and enmity by fans, official sources and George Lucas himself, who does not consider the special to be canon. Despite the relative unpopularity of the special, those at Lucasfilm responsible for licensing maintained its status as part of the continuity. As a result, from 1978 to 2014, most elements of The Star Wars Holiday Special fell under the C-canon — the classification given to Star Wars books, comics and games that have been officially licensed.

After Lucasfilm was acquired by The Walt Disney Company, the letter designations were retired. Most works previously under the C-canon, including all Star Wars novels written before that point, were removed from the canon and placed under the Star Wars Legends banner instead.

Possibly the Terminator franchise:

CAMERON This is a continuation of the story from Terminator 1 and Terminator 2. And we're pretending the other films were a bad dream. Or an alternate timeline, which is permissible in our multi-verse. This was really driven more by [Tim] than anybody, surprisingly, because I came in pretty agnostic about where we took it. The only thing I insisted on was that we somehow revamp it and reinvent it for the 21st century.

And to some degree Cameron has been down that road before:

Earlier this month, James Cameron claimed that Terminator Genisys, the fifth entry in a sci-fi franchise he created with 1984’s The Terminator and 1991’s Terminator 2: Judgment Day, was “in my mind…the third film.” It was a bold endorsement of a film to which he had no direct involvement. But more crucially, it was a silent yet unmistakable condemnation of the series’ third and fourth chapters, 2003’s Terminator: Rise of the Machines and 2009’s Schwarzenegger-free Terminator: Salvation, neither of which had his imprint. With his comments, Cameron sought to eradicate those two installments from the series’ official canon—which rather ironic, given that director Alan Taylor’s Genisys goes out of its way to not only diminish the importance of Cameron’s works, but to outright erase them.

In television the 9th Season of Dallas aired from 1985-1986 but was retconned away as a dream Pamela Barnes Ewing had, in the opening of the 10th season, thus becoming known to fans as "The Dream Year" or "the Dream Season". I believe that this was done because many fans were upset by plot developments in that season.

In movies the James Bond series was rebooted with Casino Royale in 2006. Thus Casino Royale (2006) and its sequels are not sequels to the previous James Bond films from Dr. No (1962) to Die Another Day (2002). And Casino Royale (2006) and its sequels do not happen in the future of the previous James Bond films from Dr. No (1962) to Die Another Day (2002).

And within the sequence of James Bond movies from Dr. No (1962) to Die Another Day (2002) there are two special cases. Casino Royale (1967) was produced by different persons and had a different plot and continuity from the James Bond movies produced by Eon Productions. Never Say Never Again (1983) was also not produced by Eon Productions and has the same basic plot as Thunderball (1965). Thus Never Say Never Again (1983) and Thunderball (1965) might be considered alternate universe versions of the same story.

But I don't think that any of those alternate universe versions or reboots is due to fan dissatisfaction with the course of the James Bond Series.

In the Star Trek the four movies made in the 1980s were a series of sequels. Star Trek II: The Wrath of Khan (1982) was a sequel to the TOS episode "Space Seed". Star Trek III: The Search for Spock (1984) was a sequel beginning soon after the ending of the previous movie, and ending with the protagonists on Vulcan. Star Trek IV: The Voyage Home (1986) opened in the "3rd month" of their Vulcan exile, as they prepare to return to Earth and face the music for their actions in the previous movie; and ends with Kirk getting a new ship the USSS Enterprise 1701-A. Star Trek V: The Final Frontier (1989) is less connected to the previous films but begins with the new ship having a lot of problems.

In Star Trek fandom Star Trek: The Motion Picture (1979) and Star Trek II: The Wrath of Khan (1982) are often divisive, with fans arguing about which was better. And many believe that the creators of Star Trek II: The Wrath of Khan (1982) deliberately ignored Star Trek: The Motion Picture (1979) and more or less tried to retcon it out of existence. Similarly the creators of Star Trek VI: The Undiscovered Country (1991) may have ignored Star Trek V: The Final Frontier (1989) and wished it had never been made. Star Trek VI: The Undiscovered Country (1991) mentions events in Star Trek II, Star Trek III, & Star Trek IV, but doesn't mention any events from Star Trek V.

Gene Roddenberry, creator of Star Trek, considered that some of the plot elements in a particular movie or TV episode could be canonical while others were not canonical. Roddenberry considered Star Trek: The Animated Series (1973-1974) to be canonical until he decided it wasn't canonical, and considered some aspects of Star Trek V: The Final Frontier (1989) and Star Trek VI: The Undiscovered Country (1991) to be non canonical.

Thus many fans and creators of Star Trek consider some movies, episodes, and TV series to be non canonical. Of course Paramount is happy to continue making money from even the most despised and controversial Star Trek movies, series, and episodes and would never think of decreeing any Star Trek production to be non canonical or not worth watching.