Starting in 2014, all but two of NJ Transit's original GP40PH-2s have entered an in-house rebuild program by NJ Transit for a mechanical conversion into a standard GP40-2 for non-revenue service. The HEP motor was removed, unlit number boards were drilled in, the rear ladders were removed and replaced with steps, and LED markers were applied to the rear end of the locomotive, replacing their original tri-color class lights. As of 2020, locomotives 4100, 4101 and 4109 are the only ex-CNJ locomotives that remain in service, along with NJ Transit's GP40PH-2B units and Metro-North's GP40PH-2M unit. The GP40PH-2A units were retired upon the delivery of the ALP-45DP, and they have since been stored, except for one unit, which was sold to MARC.