Conrail cars that were transferred to CSX were lettered NYC. The cars transferred to NS kept their CR reporting marks. Locomotives transferred to NS were lettered PRR, and locos transferred to CSX remained as CR.
The reason for use of those reporting marks, besides the fact that the "ownership" of the reporting marks was transferred through Penn Central to Conrail and then to NS/CSXT, is that for at least the first five years after the split of 1999, Conrail Inc. and all of the former Conrail property was jointly owned by NS and CSX.
Both railroads set up operating entities for their parts of Conrail. The NS part was or is operated by an organization owned by Conrail, Inc. called "Pennsylvania Lines LLC" for "Limited Liability Corporation." The CSX part was or is operated by "New York Central Lines LLC." NS and CSX selected those names, certainly with total awareness of their historical significance.
I have not kept a close eye on the current status of Conrail, Inc or its subsidiaries, but it still exists and operates the Conrail Shared Assets Orgainzation for the three terminal areas.
So that is the long story on why some former Conrail cars on CSX are lettered for NYC. They could use TOC, B(&)A, LSMS, U(&)D or RW(&)O if they wanted to, as long as no other road has pre-empted the use of those reporting marks.
Gordon Davids