It will take up to five years to replace everything in the signal control room, but full service is expected to be back within nine months to a year.
The short answer is that most of the equipment dates back to the 1930s and consists of extremely complex circuits and mechanisms. These things are custom-built and must now be rebuilt from scratch. More than 600 relays and circuits were destroyed in the fire, and each one has to be redesigned, rebuilt and replaced without shutting down the rest of the system.
It would be near-impossible to replace the entire signalling system without essentially rebuilding the railroad, and that would require severe disruptions in service. The A and C lines share track with the B and D for five miles in midtown, there is a complex junction with the eastern IND system at West 4th Street, and small but complex sections of track are shared with the G and F in Brooklyn, not to mention the E running on the Queens Blvd line with the F, G, R and V for ten miles or so.
Whatever you do to the A and C in order to rebuild will aversely affect all those other lines. If you make schedule changes, you have to make changes on other lines to compensate. If you change routings, you have to reroute other lines so a given section of track is not occupied beyond capacity. If you shut down the downtown local track, it not only affects A and C riders from upper Manhattan, it affects B and D riders from the Bronx as well.
In other words, a great deal of the extended timeframe comes from the complexity of repairing a system that must work 24/7 with minimal disruptions to other lines.
Another point glossed over in the pit thread is that the MTA has made significant, albeit limited progress in rebuilding signal systems. The subway has gone from being controlled by nearly a hundred switch towers all over the system to around a dozen centralized towers, and the Canarsie line has had its signalling system entirely replaced with a computerized one that in a couple years will begin to completely automate train service on that line. (The Canarsie Line (L) is isolated, not directly connected to any other revenue track, meaning it’s easier to replace the signalling system with minimal disruptions.) The Flushing (7) and Brooklyn-Queens Crosstown (G) are next, assuming the CBTC system on Canarsie is succesful. After that, the major sections of the IND and BMT would be converted in small increments, a process taking years and many, many dollars.
So, in short, it’s a very complex thing to fix.