Harry could try to communicate openly with his mates. He can explain his side of the story and clear up any misunderstandings. This might be difficult at first, but it's a direct approach.
One possible reason could be jealousy. Maybe Harry has some special abilities or has received more attention than his mates, which makes them envious. Another reason might be a misunderstanding. Harry could have been misinterpreted by his mates due to some miscommunication or false rumors.
Well, it could be that Harry Potter makes a big mistake in fanfiction. For instance, he accidentally endangers his mates. This would lead to them feeling angry and rejecting him. Also, differences in beliefs or goals can play a part. If Harry starts to pursue a path that his mates don't agree with, like getting too involved with a certain type of magic that they consider dangerous, they might reject him.
Harry could try to find out the root cause of the rejection. He might start investigating if there are any external influences on his mates. He could also reach out to other characters for support, like some of the Hogwarts professors. And he might try to prove himself to his mates, by showing them that he's still the same Harry they used to know deep down.
He might be initially heartbroken. Harry has always been a bit of an emotional person, so he could go into a state of depression for a while. He might isolate himself from his friends and focus only on his studies or fighting against the dark forces, using it as a way to distract himself from the pain of the rejection.
It might also be Neville. He has shown great courage and loyalty in the series, and he would surely step up to comfort Harry. Neville has a kind heart and would be sensitive to Harry's pain.
He might be shocked at first. It's not every day you find out you have mates. He could be a bit clumsy around them, not knowing how to act. Maybe he stutters when he tries to talk to them or gets all flustered.
They could also create a peaceful and relaxing environment for him. Maybe they clean up his room, light some scented candles, and just sit with him in silence. This kind of quiet presence can be very comforting. They might also write him little notes of encouragement and leave them where he can find them easily.
Perhaps the father is under the influence of some external force. In fanfiction, it could be that he is being blackmailed or controlled by a dark wizard. As a result, he has to reject Harry against his true feelings. Also, it could be that the father has made some big mistakes in his life and he doesn't want Harry to be associated with him because he thinks it will bring harm to Harry.
One reason could be that his mate has different life goals. Maybe she is more focused on her own magical career and doesn't see a relationship with Harry fitting into that at the moment. Another possibility is that there are misunderstandings between them. For example, Harry might have been too involved in some dangerous adventures and his mate thought he didn't value their relationship enough. Also, it could be due to external pressures, like her family or friends not approving of Harry for some reason.