Merlin might become more confident as Harry Potter. In his past life, he was often hiding his magic, but as Harry, he can be more open in the wizarding world. So he could be more assertive in dealing with challenges.
There could be a new love interest for Merlin. This character might be a powerful sorceress who initially clashes with Merlin but then falls in love with him. She could have her own set of powers and a backstory that is intertwined with Merlin's new journey. Also, there might be an old character from the original series who has also been reborn in some way, like Morgana. Her new incarnation could have a different role, either as an ally or a more complex antagonist to Merlin.
Often, the theme of Merlin regaining his lost power or finding new ways to use his magic in his'reborn' state is explored. This can involve him having to learn magic all over again in a different magical environment. It might also include themes like redemption, where he tries to right the wrongs that happened in his past life, like finally fulfilling the prophecy of bringing back the Golden Age that he and Arthur were supposed to create.
If Merlin is reborn, it would likely shift the power balance significantly. His knowledge of ancient magic is vast. He could potentially teach new spells and techniques to the younger wizards, giving them an edge over the dark forces. For example, he might introduce powerful defensive spells that could protect Hogwarts better than the existing ones.
Well, perhaps Merlin's reborn identity as Harry Potter means he has an innate understanding of certain things. He could be able to see through Voldemort's plans more easily because he has seen similar dark wizards in his past life. Also, his relationships with the other characters like Hermione and Ron would be different. He might be a mentor - like figure to them, guiding them with his centuries - old wisdom.
One great female Merlin fanfic could be one where she uses her magic in unique ways to save Camelot. For example, in a story she might use her powers to heal the knights secretly when they are injured in battle. This would add an interesting twist as she has to hide her actions from Uther.
If Merlin died in the fanfiction, it could trigger a series of tragic events. The balance of power could tip, and the villains might seize the opportunity to attack. It could also bring out hidden strengths in the remaining characters as they try to cope with the loss.
One idea could be that Merlin is reborn as a student at Hogwarts. He could use his ancient magic knowledge to solve some of the mysteries that even Dumbledore has trouble with. For example, he might be the key to understanding the true nature of the Chamber of Secrets in a way that no one has thought of before.
In a more humorous take on the 'Merlin tied to a bed' fanfiction, it could be that Merlin has fallen ill and the overly - protective Gaius has tied him to the bed to make sure he rests. Merlin, being the active person he is, complains constantly. Arthur comes to visit and teases Merlin about finally being still for once. Meanwhile, Merlin tries to convince Arthur to let him loose, promising that he'll be fine. Eventually, Gaius relents and unties Merlin, who then immediately starts bustling around the room.