He could have been focused on his studies at Hogwarts. Schoolwork, learning magic, and preparing for the challenges ahead in the wizarding world took up a lot of his time and energy, leaving no room for fanfiction about his own house.
Maybe he was too busy dealing with the real threats in his life, like Voldemort and his Death Eaters. Fanfiction might seem unimportant compared to the real battles he had to face.
Maybe it's to fit certain moral or ethical standards set by the fanfiction community. For example, some interpretations of Harry's character might be considered too dark or out of character, so they censor it to keep the overall tone positive and in line with the general perception of Gryffindor values.
One possible reason could be a major disagreement with the Gryffindor house leadership or some of the students. Maybe he feels that they are not living up to the values he thought they held. Another reason might be that he discovers some dark secret within Gryffindor that makes him uncomfortable and he decides to leave.
One reason could be that he doesn't like the spotlight that comes with being a Gryffindor. In the original story, Gryffindors are often in the limelight, and in fanfiction, he might be tired of all the attention.
Perhaps he leaves Gryffindor in fanfiction because he is influenced by a new mentor or friend who is from a different house or group. This person might convince him that he can achieve more or be more true to himself outside of Gryffindor. Also, it could be due to a prophecy or a special mission that requires him to distance himself from Gryffindor for a while to protect the house or the entire Hogwarts from a certain threat.
In the world of fanfiction, many readers have specific expectations based on the source material. Since J.K. Rowling created Harry Potter as a male, some fans may be less interested in a female version. Additionally, there might be a lack of exposure for Fem Harry Potter fanfictions. If they're not promoted well within the fan community, they tend to be ignored.
It might be ignored because it has a very unoriginal plot. Fans are looking for something new and exciting in fanfiction, not just a rehash of the original stories.
There could be several reasons. One is simply to add drama. A lot of fanfiction writers thrive on creating conflict, and what better way to do that than by taking on one of the most beloved houses in the 'Harry Potter' series? Another reason might be personal bias. Perhaps the writer had a negative experience with someone who identified strongly with Gryffindor, or they just don't like the traits that are typically associated with Gryffindor, like impulsiveness, and they use fanfiction as a way to express their views.
Maybe he just doesn't like how some fanfictions distort his real experiences in Gryffindor. He might feel that they don't accurately represent his relationships with his housemates or the true nature of the Gryffindor house.
One possible reason could be a false accusation of using dark magic. In some fanfictions, the wizarding world can be very paranoid about dark magic, and if Harry was wrongly suspected of delving into it, Gryffindor might exile him to protect their reputation.
In some fanfictions, the author might create a situation where Harry's actions lead to great harm to Gryffindor as a whole. For instance, if he makes a decision that causes Gryffindor to lose a significant amount of points in a crucial time, like right before a major competition. This could lead to his censure as the house would see him as a liability. Also, if he gets into a feud with important Gryffindor figures, like the prefects or the head of the house, it could result in his censure.