The C-Liners and H16-44's all disappeared rapidly in late 1963 and early 1964. The ALCO Century replacements were bought at the time of the NY World's Fair, and the connection of a modernized railroad was smooth. As the F-M's disappeared, some of their parts were taken and re-used in the new locomotives, but which parts, I have no idea. The locomotives themselves were shipped to a scrapper, where their prime movers were salvaged. Some went into oil rigs in the southwest, others went into marine applications. The latter is interesting, because they wound up in Viet Nam, and when the Communists won the war, they got the abandoned equipment! Consider those prime movers of 60 years ago, once hauling New York commuters, now hauling Viet Namese Commies!
Anyway, the locomotives were traded in on the new ALCOs of 1963-64. They had a terrible maintenance history, and were constantly in the shop to be rescued. Access to the engines was miserable. Like other railroads, once the green light was given to lose the FM's, the railroad was only too glad to oblige.