Would the whole of the subway system below sea level be filled or is there some safeguard to prevent this happening?
Something similar happend in the Capital of the Czech Republic, Prague, in 2002. They have an extensive underground metro system, with some very deep stations. When the river Vltava flooded, the metro acted like a drain, and many stations were completely submerged. Not actually due to a failure of a line or tunnel, but same result.
It must have been a complete nightmare pumping out the water, cleaning everything, before the job of renewing whole signalling and safety systems. Bit by bit, the system was restored to full operation, but it took several months before all stations were re-opened. Luckily, many of the metro trains are robust, Ruskie built units, which weren't too badly damaged.
I am a regular visitor to Prague and the Czech Republic. The flood happened in the summer, but by the time we visited in late autumn, everything was back to normal and we were able to travel between pubs unimpeded.
This video shows the extent of what happened. Check (or should that be Czech
)-out the shot of the top of the escalators at 2 mins.