The problem wasn't with National Rail website per se.
The release of Darwin 4.1 on Wednesday the 4th of September was to improve GPS data.
Turns out something messed up during the release, so knocked out real time running information for everywhere. Any information from 21:00 on the Wednesday may not have been up to date.
05:03: Suppliers alerted that no live information was being presented on journey planners or mobile applications.
06:30: Suppliers continuing analysis and monitoring.
08:30: Cross party call arranged for 08:45. Further communication to be sent after this meeting.
09:15: Decision reached to roll back to Darwin v4.0. Estimated timeframe - 1 hour.
10:34: Final phase of rollback being completed. Estimated time for completion - 30 mins.
11:49: Users advised to disconnect (if they have connected) to Darwin as information still unable to display.
12:54: Darwin v4.0 restored.
Other services may have come back online earlier or users (TOCs) may have had their own way of updating services.
Factoid: Darwin is a system that takes real time data about trains from a bunch of sources and pushes it out to everywhere - all mobile apps, websites (inc National rail) and CIS screens. The drive was to ensure data (how late a train is for example) is consistent between online and the station screens.