Another way? You mean there's *another* linked network of devices capable of channelling massive amounts of dark energy, spread throughout the galaxy and all controlled from a central hub? Well why did you say so!?
As for what the Catalyst did and didn't know; it's not omnipotent. Never claimed to be. If they had reason the believe the plans were still out there, then they would have made sure that they were eradicated before they returned to dark space. The fact that they didn't means they had no reason to have such a belief. QED.
They also didn't know that Javik survived. That the facility on Ilos managed to wait out the Prothean extinction and board the Citadel. Or that the Leviathan were still out there in hiding. Honestly, those seem to be greater oversights then the existence of some encrypted data file buried in a massive archive that's damn near impossible for non-Protheans to even comprehend, much less decipher.
That aside, being aware the organics are building something they think will wipe out the Reapers isn't the same as actually knowing how it works, or even caring. Indeed, when you speak to the Catalyst, it's implicit that it's just then analysing it's capabilities. Something it couldn't do until after it had engaged with the Citadel.
Remember that the Catalyst is an AI. It thinks like a machine. After a billion or more years, tens of thousands of cycles, it's had a 100% success rate in it's harvests. It not capable of being paranoid about what else *might* be out there the threaten it because so far nothing has. It can only conceive of such possibilities in terms of infinitesimally small statistical provabilities. In short: "no data available".