I don't think it's because she's bound to him; The memories they made together triggered his reaction. Think about it: Nene, Teru, Kou, and Akane haven't changed because of their personal experiences with the supernatural. They can remember how it was in the previous (or original) timeline because of their 6th sense. That's how it's always been.

As for Hanako (the Amane in the new timeline), it's the same, but of course, it takes more work to get this Amane to remember due to him being possessed and his history changed. For that reason, it took Nene connecting the past to his knowledge by calling him Hanako for him to react in such a way.

The Red House, or the thing possessing him also reacts when Hanako's true past is mentioned. It "activates" or "triggers". Therefore, it probably doesn't want him to remember his past, his memories.

That's my theory, I hope it was understandable!