If you are right and the anomalies that they are detecting are indeed the Flood, then in all likelihood, they are coming back with a vengeance.
Unbeknownst to the humans, they had not actually found a cure; the Flood had chosen not to infect the humans instead; The precursors who were now the Flood allowed the idea of a cure to gain credence, so that in the future more efforts would be diverted to attaining it rather than simply excising the infection. When the Flood returned, the Forerunners—Who had devolved humanity and destroyed its civilization—were entirely unprepared to challenge the Flood properly
If the Flood could do this, then what stops them from coming back? If a Gravemind formed on Installation 05 then logically, a Key Mind may have formed somewhere else in the galaxy.
I would have more, but most of the articles I click on are 6 year-olds arguing about why the Flood as an enemy suck and shouldn't be put back in the game at all.