At first, it would become very strained. Harry might avoid Lupin at all costs. He would no longer trust Lupin and would be suspicious of his every move.
One interesting fanfiction idea could be that Snape discovers a hidden Horcrux that Lupin unknowingly has in his possession. Harry Potter then has to figure out how to destroy it without harming Lupin. This would add a whole new layer of drama and mystery to the existing lore of the Harry Potter world.
One great fem Harry Potter and Remus Lupin fanfiction is 'A Different Path'. It explores an alternate universe where Harry is female and her relationship with Remus develops in a very interesting way. It delves deep into their characters and how they interact in a world full of magic and mystery.
One great 'Harry Potter - Arsene Lupin' fanfic is 'Lupin's Legacy'. It delves deep into Lupin's past and his relationship with the other characters. It shows how his werewolf nature affected his life at Hogwarts and beyond in a really interesting way.
Maybe in that fanfic, Lupin did something that Harry considered a betrayal. For example, he might have made a decision that put Harry or his friends in danger without consulting them first.
One possible reason could be his self - loathing due to his werewolf condition. He might think he's not good enough for Tonks and that she'd be better off without him, fearing that his lycanthropy could bring danger or a difficult life to her.
There's a fanfic called 'Teddy Lupin: The Next Generation'. This one delves into Teddy's role in the post - Voldemort wizarding world. It details how he uses his unique abilities, being a Metamorphmagus, to solve various mysteries around Hogwarts. It's full of action and interesting character interactions.
When thinking about his own difficult past as a werewolf. Memories of being ostracized and feared by others could resurface. He might cry as he reflects on all the pain and loneliness he had to endure throughout his life.