As I recall, the BNSF has trackage rights into the JIT, so in a sense the Santa Fe has never left Oakland.

If you're thinking about the industries served out of the yard next to 34th St. that lasted until the mid 1990s or so. In her book Railroad Noir, Linda Nieman relates how she got "fired" working a flagging job at 34th St for the new freeway construction. The incident involved one of the Emeryville Locals out of Richmnond, which was using trackage rights over the SP between Stege and 34th St. These are/were the trackage rights which replaced the line through El Cerrito, Albany, and Berkeley.