I suspect that the backup mode mentioned in the article is the engine controller's secondary mode, a mechanical engine management system that uses conservative vane, fuel, and pressure settings to keep the engine running when it's suffering a malfunction or is damaged. The primary engine control is typically a complex digital controller that boosts efficiency and thrust by quite a bit, but if the engine goes outside it's programmed parameters for whatever reason, the whole thing might shut down. That's where the secondary controller comes in.
If the hydrazine-fueled emergency power system hadn't come online, they probably wouldn't have been able to level off to eject or even make a controlled glide.