I think there's confusion here on a few different levels... let me see if I can clarify:
- Train arrives from HAR engine first, so the engine is on the southern end and the cab car is on the northern end
- Problem with cab car discovered, so they decide to wye the train
- The mistake happens and it overshoots where it was supposed to stop on the SEPTA line
- Instead of wye-ing, the train goes into PHL engine first again, so again the engine ends up on the southern end and the cab car on the northern end
- In order to get to NYP, the train still needs to wye because of the issue with the cab car
- Train has passengers onboard, does the wye like it was supposed to before, and heads to NYP