You mean Yuuichi and Nayuki becoming Yuuchi and Ayu?
Nayuki and Yuuichi were never together. She had a crush on him, he didn't reciprocate.

I think perhaps you are referring to the very end, after Yuuichi has run off to the room Ayu lies comatose in, no? The scene afterwards is of the near-ish future with Ayu on the bench, who has obviously recovered (with a bag over her head ^_^ to hide an overzealous hair cut). There was no 'replacing' of Nayuki as you mean it. It's the classic 'cut to a future scene' epilogue.

Ok so if Ayu was suppose to being accoma for the past 7 yeras, then who is that Ayu that hangs out with Yuuichi and Nayaki. Is she his imagination, or is that Ayu, the real Ayu's sprit or somthing

The show kind of has a supernatural element to it. Makoto for example. I think the Ayu he meets is really there. She's created from his past promises and memories that he lost. But she doesn't really exist in the world. She mostly does familiar things in familiar places from their past. She's stuck in the time when he knew her. She disappears once the reality of her nonexistance comes to light (There is no school where she thought there was). That kinda help?

EDIT: As said below, "miracle" is a good way to put it.

For some reason, in this anime, there is a power that makes miracles happen. That is how come Makoto could become human, how Mai is fighting with demons, and that is also why, even though Ayu is in a coma, she can walk around in the real world. As you know, Ayu had been in a coma ever since the time she fell out of that tree so many years back (the last time when Yuuichi was there). Ever since that time she has had the power to walk around in the real world, reliving a simple life, waiting for the day when Yuuichi would return to fulfill his promise.

As she interacts with Yuuichi, though, she begins to dig deeper into her memories and her past, and begins to discover, little by little, that something isn't right, hence she begins "looking for something". This finally comes to a head when they go to the spot where she thought her school was, only to discover that it wasn't there, and they remembered her accident. It was then that she realized that she wasn't really alive - that this was, in a sense, all her dream. (This is a sort of universal story convention. In North American comics, the character doesn't fall off a cliff until they look down. In this anime, she can only stay in her dream as long as she believes in it. Once she realizes that she's dead, she can't manifest in physical form any more.)

Yuuichi believes that she is gone forever, until the very end when Nayuki discovers Ayu at the hospital. Once they're re-united, Ayu is able to come out of the coma, remembers all that has happened, and they are able to begin their true future together.