Another reason might be that Merlin is hiding something from Arthur. He could be flinching because he's afraid that Arthur will discover his secret, such as his true magical abilities. In the fanfiction world, if magic is still a dangerous thing to be associated with, Merlin would be constantly on edge around Arthur.
It could also be due to some past trauma. Perhaps Merlin has been through an experience where Arthur was involved in a way that now makes him flinch. Like, Arthur might have accidentally hurt Merlin during a battle training in the past, and now Merlin flinches whenever Arthur makes a sudden move.
If not resolved, it could lead to a breakdown in their relationship. Merlin's flinching might eventually push Arthur away, making him feel like Merlin doesn't trust him. This could cause Arthur to distance himself from Merlin, which would be a huge change from their usually close bond in most Merlin - Arthur stories.
Perhaps it's due to his discomfort with sudden changes or surprises. Bilbo is a hobbit, used to the simple and predictable life in the Shire. In fanfics, when he's exposed to the chaos of the outside world, like unexpected magic or the presence of strange creatures, he might flinch as a reaction to this discomfort. This shows his struggle to adapt to new circumstances outside his comfort zone.
It could be that Gwen unknowingly has some sort of magical influence over Arthur. For example, if there is some ancient magic tied to her lineage that she's not aware of, and it's causing Arthur to focus only on her and forget about Merlin. Another aspect could be that Arthur's love for Gwen is so overpowering that it's subconsciously pushing out other important relationships, like the one with Merlin.
One possible reason could be a misunderstanding. Maybe Merlin did something that Arthur misinterpreted as betrayal or dishonesty. For example, if Merlin was secretly helping an enemy for a greater good that Arthur wasn't aware of at the time.
One possible secret could be that Merlin is a powerful sorcerer from an ancient and powerful magical lineage. Maybe his family has a long - standing connection to Camelot that has been kept hidden.
One possible reason could be a magical curse. In the world of Merlin, there are many dark sorcerers who might target Arthur. Another reason could be a poisoned weapon. If he was injured during a battle, the poison on the blade could make him sick. Also, it might be a result of some ancient plague that has resurfaced in Camelot.
Jealousy could be another factor. Arthur might be jealous of Merlin's magic or the attention Merlin gets from others because of it. This could create tension and ultimately result in a break - up in the fanfiction.
There could be several reasons. He might have been ostracized by his community, feeling all alone. Or perhaps he had made some terrible mistakes that he thought were unforgivable. Another possibility is that he was under a great deal of pressure, such as being expected to fulfill some impossible task and seeing no way out.
One possible reason could be a magical curse. In many Merlin fanfictions, magic is often used as a plot device. A dark sorcerer might cast a spell on Merlin to make him forget certain things, perhaps to prevent him from using his powerful magic to oppose them. Another reason could be a self - imposed forgetting due to trauma. Merlin has witnessed and endured a great deal of pain and suffering. To protect his own mental state, his mind might subconsciously block out certain memories.
Well, Arthur could feel betrayed at first. He has been brought up to believe that magic is bad, and here his closest friend has been hiding this big secret. However, as he realizes how Merlin has saved his life and the kingdom many times with his magic, he might come to accept it and even see the potential of magic being used for the good of Camelot. For example, Merlin's magic has defeated many enemies secretly, which Arthur might now understand as a necessary protection for the kingdom.