Here are my thoughts concerning the Flood in Halo 4.
According to the history of the Forerunners, they activated the Halos a long time ago and wiped out the Flood, all sentient life in the Milky Way Galaxy and most of themselves. However, despite this, the Flood somehow survived.
At the end of Halo 3, we assume the Flood was destroyed. However, we don't know this for sure.
I have a theory that the Halos can wipe out minor Flood, but can't do anything to the Gravemind. I think every time the Halos are activated, the Gravemind restarts the Flood.
I also have a theory that the Flood are a manufactured system put in place to cleanse and purge the galaxy as part of a cycle, for whatever reason, and I think the Flood are either products of the Precursors or the Precursors themselves.
I don't know if we'll see Flood in Halo 4, but I'm sure we'll at least hear about them or learn new things about their origins.