I was around Whippany on Saturday and briefly on Sunday and saw the derailment site from a distance. While the decision to go east was, in hindsight, a bad one I leave that to M&E's internal workings to review where communications failed about conditions in the area. That said I give management and employees extremely high marks for how the situation was handled in an orderly and professional manner. They got the people off and back to Whippany using the FL9 and their two cars that remained on the track in two runs. Everyone remained cheerful and upbeat and professional in their dealings with members of the public. (Remember that this is largely a small child/parent event - the possiblities for screaming children were endless. I didn't see any and I have a low tolerance for screaming kids - I'd have noticed.)
Once the crowds were gone they set about trying to make things as right as possible for their other customer - the museum - by pulling out everything they had direct control over at Whippany to make Sunday's train. At that point they didn't know how many, if any, of the NJT coaches would be available. They fired up the other FL9 to return to derail site and on Sunday the (unfortunately filthy) 18 the cover the passenger job. (choice of 1 FL9 and the 4228 was probably based on both FL9 currently facing west).
I imagine that the events for the museum are contracted at breakeven to a small profit. (An old board post from Mr. Fuller said they contract by the year) Between the extra locomotives, calling in staff on OT and the physical repairs it was an expensive weekend for the M&E. Nevertheless they did it with style. Mr. Fuller, in particular, was (at least outwardly) an unruffled COO taking care of business. That gets high marks in my book.
Will this hurt them in Union - maybe. But the base issue of a mechanical failure of track structure is minimized (it can never be totally alleviated) by the rebuilding going on prior to train operation. The extensive work underway on the Whippany line, when complete, should remove concerns there as well for future museum events.