Actually, i think that the Forerunners didn't know about the Flood. They would have prepared themselfs for such a terrible enemy. Instead, when the Forerunner-Human war started, they didn't know why were the Humans invading their territory. Only when they defeated them, they understood the Humans were fleeing from the Flood, and when it infested the Forerunners colonies they didn't know how to fight it. Then they discovered the Humans had a "weapon", something to use against the parasite, and that would have stopped it.
But they had already de-evoluted them, and while their colonies were falling, they tried to take some flood spores to study them and to understand how could the Humans had fought them.
But while they (the Builders and Mendicant Bias) were testing the Halo array on an abbandoned Human World, they discovered something. A living being, a prisoner, that proclaimed himself as the last of the Precursors. Immediately, they put Mendicant Bias to ask him who was him, where he came from, and stuff like this. Probably, they also asked him how could they stop the Flood.
But they didn't like the answers. He revealed something to them, something we don't know (probably what was the Flood, or how should the Forerunners end this conflict), that made Mendicant Bias go crazy, like in a rampancy stage.
This is why i think they didn't know about the Flood. IF they knew everything, why should they put an advanced AI to ask questions to a so-called Precursor? Why should they fight the Humans, if they knew that MAYBE the Flood was still alive?
And the Precursors didn't left the galaxy. They were forced by the Forerunners that rebelled against them to flee away, and the last survivors are hidden in the boarders of the Milky Way. This is what the Primordial One reported.
Wich was a Gravemind of Precursors.