I think they retconned it...Due to a badly thought out plot...Or it could have been possible that Cortana misunderstood what the halos were capable of doing as it is the first 'known' forerunner construct as that was said in Halo CE...
Than there is also the undeniable fact that the flood was essentially the precursors in another form, which by the definition of the forerunners, were a tier 0 species and literally their 'gods' being the race who created them along with humans, which tried to wipe the forerunners out after deeming them 'unworthy' of the mantle and humans should be tested next. Forerunner found out, and tried to wipe out the precursors, succeeded to an extent, than the precursors decided to take revenge and took the form of the flood to, as spacebattle forums put it, troll the shit out of the forerunners. So in doing so they decided to turn themselves into a powderlike organic compound and put themselves in a random ship and let it drift through the milky way for no aparant reason, eventually a tier 1 human-san shyuum alliance found it, though I am not sure if this was an accident or if they did it on purpose, and began conducting expiriments on the powder. Eventually it was found to have a pacifying effect on pherus, a popular pet, and a popular delicacy among San shyuums, so they fed it to the pherus not knowing what it was. It took centuries for the flood to evolve, and when it finally got to that point...I think you can see what happens.
But anyways, ignoring the top bit, which is mostly irrelevent to this question, the flood being the precursors could have easily turned back to their original precursors form with the forerunner industry and the remaining precursor tech under their control, the flood was more or a mean to an end, they lacked the numbers but wanted to utterly slap the forerunners across the face, hence the flood, though I believe they didn't predict the halos, as that will be able to kill and possibly destroy anything with a significant nervous system or a brain, hence all known precursor tech, gravemind, keyminds, pure form, combat forms, and possibly even infection forms, leaving only free floating flood super cells at best, which could be easily cleaned up by sentinels, hence reverting the flood back to the feral stage, where they are basically zombies on steroids.