By the 2000s, a highway interchange realignment had rendered San Diego less accessible. One of the newer overpasses even encroached onto the site causing its adjacent Chevron station to be removed. Although the former Motor Lodge was able to remain in business, its attached Restaurant wasn't so fortunate. Based on modifications evident on the buildings facade, the former HJ had operated as a Big Boy and then likely was a Coco's before falling into oblivion.

Good Night to the Good Nite: Located within the Navajo Community Plan Area, at a mid 2006 meeting local officials quietly rezoned San Diego's site to allow for its demolition. William Lyon Homes, Inc. has been approved to construct 100 residential condominium units with amenities at the site.