Salt water damage is likely behind the extended delay.
Seawater can be very corrosive for systems and materials never designed to deal with salt water immersion. Even when limited to short term exposure.
The subway tunnels have to be drained and everything should be given a freshwater flush before/during repairs.
Proper water tight storm gates at all of the tunnel access points would have limited the damage. Backed up by independently powered pumps the tunnels might have stood a chance of seeing a fast post storm recovery.
They did not even move the train cars to high ground. A few hundred of them ended up in up to 6 feet of salt water in a rail yard. The electric motors on all of them are under the cars. It may be months before those cars are usable.
