It could be a spell gone wrong. Maybe some dark magic or a misfired charm affected her memory. It's not uncommon in the wizarding world for things like this to happen.
Another reason could be some sort of psychological block. Maybe there was a recent argument or a big stressor in their relationship that she subconsciously doesn't want to deal with, so her mind just blocks out the fact that she's married to Harry.
One possible reason could be a spell gone wrong. Maybe she was experimenting with some new magic and it backfired, causing her to forget she was a witch. Another reason could be some kind of magical amnesia brought on by a powerful dark force or a magical accident.
In fanfiction, Hermione's obsession with Harry could stem from her own insecurities. She may see Harry as someone who is more confident and free - spirited. She is obsessed with him as she wants to be part of his world, which seems more exciting compared to her own studious and rule - following nature. Additionally, their friendship has a strong foundation, and the writers of fanfiction might exaggerate this into an obsession to explore different storylines.
One possible reason could be if Harry takes a big risk without consulting her first. In the wizarding world, their adventures are full of danger, and Hermione is often the cautious one. If Harry jumps into a situation like facing a powerful dark wizard alone without a proper plan, Hermione would likely blame him for being reckless.
I'm not sure specifically as there could be many different versions of such a fanfiction. It might involve some kind of emotional journey where Harry and Hermione face difficulties and try to move past painful memories, perhaps related to the battles they've been through in the wizarding world.
One possible reason could be that Hermione sees Harry more as a friend. She has a deep, platonic bond with him and doesn't want to risk ruining that friendship by turning it into a romantic relationship. In the original story, they have been through so much together as comrades in the fight against Voldemort, and she may value that camaraderie above all else.
One possible reason is that the fanfic writer wants to create conflict. By making Hermione not believe Harry, it adds tension to the story.
One possible reason could be a creative plot twist by the fanfic writer. Maybe they want to explore how Harry would grow and develop on his own without Hermione's support. Another reason might be to introduce new and different story arcs that involve separation, like Hermione having to leave for a dangerous mission that she can't involve Harry in.
In fanfics, the relationships between characters can be explored in new ways. If the fanfic writer decides to show a rift between Hermione and Harry for the sake of drama, they might create situations where Hermione doesn't believe Harry. This could be due to a series of miscommunications or actions that Harry takes which seem out of character to Hermione.
Perhaps in the fanfic, there is a love triangle situation involving Ron. If Harry unknowingly gets in the way of Hermione's relationship with Ron, she could develop hatred towards him. Another aspect could be that Hermione feels Harry is getting all the credit for their group's achievements, while she is doing a lot of the behind - the - scenes work, which makes her resentful.
One challenge could be finding a safe place to stay. The wizarding world is not that big, and there are many places that are easily detectable. They would need to use magic carefully to avoid leaving a trail for those who might be looking for them.