Without a gravemind, the flood can't control the ships they are on. To do that they would need a new grave mind, and that requires more bodies, and that requires control of the ship.
I don't remember what happened to installation 05, but installation 04 was destroyed, everyone on it died, and the replacement fell apart while firing, killing everyone on it. installation 00 was subject to a tactical pulse, killing everyone there as well. The flood on the other rings still exist, but they have been undisturbed for since the last time halo fired, and even if one of the sides wished to use it as a superweapon, they would have to find the ring first. Both of the rings found in halo 1&2 were found by chance.
A better question would be what happened to the brutes. They were 12 billion strong at the start of halo 3, whereas the elites had 8 billion and the humans less then .5 billion.