Well, I think it is a bit more complicated. Imagine if your very close friend, which you know for many years and have some local memes and stories, just lose their personality. They have the same body, the same voice, but at the same time they have a different character. Moreover they don't remember anything from your relationship. I think it is just psychologically difficult to build new relations with this new person, while they remember you about your good old lost friend with only their existance.
But on a happy note I think it is possible for Kotone and Feng to be friends again. Maybe we need to help Kotone to step over her sorrow memories, like we did with her tail. And I also think Feng didn't lose her memories completely, if you remember her dreams about her past life and nostalgia thing. Maybe conversation with her about who she really is and some hypnosis sessions to force her remember all her dreams will help. It isn't a perfect method, I think, but it can work.