One reason could be that he's being hidden by some powerful magic from a group that wants to use him for dark purposes. Maybe there are dark wizards who know of his future importance and want to either kill or control him, so a good wizard has made him disappear.
Perhaps in the fanfiction, Harry discovers some sort of premonition or sign that something terrible will happen to him at Hogwarts. This could be related to Voldemort or some other dark force. In order to avoid this fate, he decides to disappear. He might go into hiding with the help of some friends or allies he has made outside of Hogwarts.
It might be related to his family's past. There could be some secrets in the Potter family history that make it necessary for him to disappear. For example, there could be an old family enemy who has found out where he is, and to protect himself, Harry is made to disappear. In fanfiction, the author can create all kinds of backstories for this.
One possible reason could be that he is suffering from post - traumatic stress disorder. After all he has been through, he might want to isolate himself from the wizarding world to heal. Another reason could be that he feels a sense of guilt for those who died in the war, and disappearing is his way of punishing himself.
One reason could be that he doesn't like others taking creative liberties with his story. He might feel that it's his story and only the original version should be the 'true' one.
One possible reason could be a dark turn in the story. Maybe Harry is under the influence of a dark magic or a powerful and evil entity that makes him lose control and start to destroy Hogwarts. For example, if he was possessed by a powerful dark spirit that wanted to eradicate the symbol of the wizarding world's good, which is Hogwarts.
In some fanfictions, there could be a change in the Hogwarts admission policy. Maybe they found some supposed flaw in Harry's magical abilities or his background that led to his admission being revoked at the last minute, so he didn't arrive at Hogwarts. Also, it's possible that some other powerful magic was at work. A powerful wizard or witch could have cast a spell on Harry that made him forget about Hogwarts or made it so that he couldn't physically reach the school.
One possible reason could be that he was under the influence of a powerful dark magic or a curse that made him lose control. Another reason might be that he was tricked into believing Hogwarts was a threat to the wizarding world in some extreme way. Maybe a powerful enemy manipulated him to think that destroying Hogwarts was the only way to save everyone.
One reason could be that he has fallen in love with someone outside of Hogwarts and wants to stay with that person instead. He may feel that Hogwarts will keep him away from his beloved.
Well, perhaps in the fanfiction, Harry has a vision of a different future for himself that doesn't involve traditional Hogwarts education. He might have seen a path where he can make a greater impact on the wizarding world without the constraints of school. It could also be that he's being influenced by a new character in the fanfiction, someone who convinces him that there are better ways to develop his magic and knowledge outside of Hogwarts. This new influence could be from a different magical culture or a rogue wizard with unique ideas.
One reason could be that it doesn't stay true to the original lore. For example, if the fanfiction changes the fundamental rules of magic in Hogwarts that were established in the original series. Another reason might be that the characters' personalities are distorted. Harry Potter is known for his courage and self - sacrifice, and if the fanfiction turns him into a cowardly or self - centered character, it could be rejected.
Perhaps he has seen a dark future for Hogwarts in a vision. He might think that by staying away, he can avoid that future or protect himself from some unknown danger. In fanfiction, there are often new and creative plotlines like this.
In fanfiction, the author might want to explore a different side of Harry. He could be berating Hogwarts education because he realizes that some students were left behind. There were students like Neville who didn't really shine until later, and Harry might think that the school system should have been more inclusive and better at nurturing all types of magic abilities from the start.