Well, they likely stored them all the way from Newark to just after Harrison, as that is all elevated, then probably some more in the river tunnels & shut the flood doors, and likely up on the other lift bridge and its approaches, and more just outside the portal east of jsq and maybe a bit east of thr bridge where there are severed grade crossings. They have/had a lot of options. They installed those damn flood doors just in time, otherwise the damage would likely have been far worse, especially with the slope & depth of the downtown two tubes.
Next stop the square, journal square station next!