It sounds like they let this problem fester until it has reached this existential end. They clamor for new technology, which they get, then they use the most risk adverse management strategy and never upgrade or change it, until it reaches this problem state.
They either need significant third party help deploying and managing this system, or they should go back a few generations of technology and use the simplest possible system that meets their needs. Pen and paper should be considered if it can be made more efficient.
I guess the people who work on public transit aren't interested in having the best public transit system available. They're only interested in keeping it running for as long as possible with zero changes or responsibility.
This is why I'm strongly doubtful on public transportation in the US. Our bureaucracy can't handle it.