If SP did withdraw all of its GP9s from service in 1995, UP must have brought at least some back. I saw two (SP 3857 & 3880 if I remember correctly) working local trains out here in early 1997. When I get some time I will have to pull out some of my SP Reviews from that time as they were keeping track of the SP GP9s, SD7s, and SD9s.
Also, many shortlines still run GP9s and It seems like BNSF still has some rebuilt GP9s, albeit with new cabs.
Remember, many of the last steam ran along side the GP9’s for almost four years of so if you are considering the 54 to 58 era.
The main line use of the GP9 was pretty much over after the high horspower unit starting coming out in the mid to late sixties, and the GP9 became more of a local or branch line use by the late 70’s.
You can run a GP9-E at the Feather River Portola Muesum. I recently got the chance to do this and it was really exciting to run the unit.