When Jess comes out of the bathroom, we can see it is now in a different direction. After being located just beyond the kitchen area from the first season until now, the bathroom in Luke’s place has moved to the other side of the apartment near the bedroom area. It remains there for the remainder of the show’s run.
Compare to the bathroom at Lorelai and Rory’s house, which was permanently replaced by a walk-in closet later in Season 1.
The Annotated Gilmore Girls 