Scars are left intact, as our souvenirs. Our protagonists are unchanged.
The only stuff that carries over from the Millenium City timeline is stuff that pertains to Shingo and Kei. Their relationship developed over the course of the year as it did in Millenium City. P-users can remember what they did in Millenium City, so it was obviously real for them, but no one else they may have interacted with remember.