>>718928406
You can explain it as Chaos wasn't actually fooled at all and beat him by playing to stall the game indefinitely or by fundamentally corrupting the nature of Humanity to poison the literal flavor of faith of humans to ensure his Godhood is subverted.

Or that the Emperor knew that Chaos knew and so KNEW this would happen and accounted for it anyways because HE had faith in Humanity to break the stalemate somehow and did all this out of beneficence and his own personal faith to give Humanity a better future.