Then, in 1965, Southern Pacific Railroad had reclassified their units as EF618-1, EF618-2, EF618-3, EF618-4 and EF618-5, as well as renumbering them as 3800-3966.[2] Then, between August 1970 and March 1980, the Southern Pacific Transportation Company had rebuilt 144 of their units under the General Rehabilitation and Improvement Program (G.R.I.P) and renumbered 142 of their rebuilt units as 4300-4441 and two additional rebuilt units being renumbered as 4450 and 4451, as well as reclassifying their 142 units as EF618E-1 and classified their two units #4450 and #4451 as EF618E-2, which had left six other SD9 locomotives un-rebuilt.[2][3]
Southern Pacific SD9E locomotive #4427 is currently being used in revenue freight service on the Dakota Southern Railway.[5]
Southern Pacific SD9E locomotive #4423 (Now restored as #5472) is operational at the Niles Canyon Railway.[6]
The Portland and Western Railroad (PNWR) uses two SD9E units for switching and industry service. PNWR 1852 (ex- SP 4397) operates out of their Albany, OR Burlington Northern yard and PNWR 1854 (ex-SP 4433) is assigned to the rock train. Both locomotives are scheduled to be scrapped or rebuilt by the PNWR's parent company Genesee and Wyoming as part of a fine resolution agreement with the EPA.[7]
Southern Pacific SD9E #4414 was used on the Port of Tillamook Bay Railroad (POTB)[8] until being scrapped in October 2010 after POTB went defunct.
Southern Pacific SD9E #4450 "Huff" was used on the Golden Gate Railroad Museum[9] before being donated to Western Pacific Railroad Museum alongside Southern Pacific SD9E #4404 until being scrapped in August 2013 due to its poor condition and lack of alignment control couplers.