Each railroad agreed to supply a quota of employees and equipment to provide switching services within a "unified zone" containing 117 miles (188 km) of track.

The ATSF would also be part of a merger in 1996, forming the new Burlington Northern & Santa Fe (BNSF), and the SP and UP would merge into the current Union Pacific in February 1998.

Also in 1998, the HBL was re-organized as the Pacific Harbor Line to create a more even distribution system for shippers using the ports and the two surviving railroads (BNSF and UP).

[4] In July 2013, Pacific Harbor Line signed a new five-year collective agreement with the Brotherhood of Locomotive Engineers and Trainmen (BLET), which has represented workers at the company since PHL was formed in 1998.

[4] On March 31, 2020, Eduardo Moreno attempted to crash a PHL train into the hospital ship USNS Mercy, which was in the Port of Los Angeles to provide Los Angeles with additional hospital capacity during the COVID-19 pandemic in California, but the train stopped approximately 250 yards (230 m) from the ship.