During the 2003 blackout, how badly did it affect rail service?

ELECTRIC Trains stopped MOST where they were when power went off. Very few had reserve power to make it to next Station. About 600 trains were stranded outside the cities.

The Subway systems of a dozen cities needed to be evacuated. As far I can research only a few minor injuries to train passengers. Thousands of Subway trains in the North East with a just a few million passengers on board it was the start of rush hour. An hour later would have been much worse from the Passenger count point of view.

Diesel trains could still move under verbal orders. This was mostly to next station or to clear a crossing or move onto a siding. The switches could be operated by hand for this.

If the Signal lights go out it is assumed to be RED.

The railroad/subway back up power is concentrated in the stations and lighting in tunnels and communications. Not for train movement.

The Northeast US blackout of 2003 was widespread starting in Ohio and cascading through the midwest and northeast US and part of Canada. Specifically to answer your question many railroad signals have emergency battery or generator backup systems. This was not the main railroad problem. Most of the power units in the northeast are fully electric, receiving power from an overhead catenary system. This system went down on the busiest rail traffic area called the Northeast Corridor which connects cities like Washington DC., Philadelphia, New York and Boston.