Railroads historically have fairly competent personnel who can get rebuilt and running again after natural disasters.
The floods of 1955 all-but wiped out the New Haven Railroad in western Connecticut, but they got going again in fairly good order. The cost of the repairs, however, accelerated the line's bankruptcy which came in 1961.
The Germans rebuilt their railroads from the damages sustained in World War II.
I'm sure they can handle those from a single flood.