For some reason, I really hope not. We've seen enough of the flood and even though I wonder what next gen can do with the flood, I'm tired of them. It would just be another silly old outbreak with high stakes thats already been done like 5 times. We just need fun covenant/forerunner enemies and it'll be fine. Maybe introduce new covenant species or different promethean builds. Or even insurrectionist humans. I just really don't want to see the flood for the sake of having the flood.fun covenant/forerunner enemies? Well yeah, I remember how much "fun" I had with the Prometheans in Halo 4 and of course Halo 5 - not. It's just an jumping, teleporting nightmare.
Also: I didn't had to read any comics or books for CE to unterstand the Flood - I always got much information about the flood - but the Prometheans? Well it#s totally complicated, not at last because the campaigns of Halo 4/5 was borfing af.
Seeing the flood in HW2 is a good sign.
Let me just say that I can wholeheartedly agree with you about the halo 5 prometheans. They were terrible and I'm sure that was a consequence of the games direction changing so many times. But with that out of the way, the halo 4 prometheans were an excellent enemy with varied weaponry, classes, armor, and abilities. The only problem was they aren't really living things (unlike the flood/covenant), so of course they feel less fun to fight against because at the end of the day you're just fighting a bunch of robots. (Plus they were orange instead of the forerunner blue. RIP). And they also lacked a flying vehicle in halo 4. But that's more of a bonus in my opinion.
You also didn't need to read outside lore to understand that the prometheans are humans either... Cortana and Chief literally talk about it, and the composers effects are shown to you in game lol. Did you ever play halo CE and question the sentinels or guilty spark? Of course not. I haven't played HW2 so I can't speak on that game but I am just tired of seeing the flood, at least as a galactic threat, which is a problem because they always are no matter how small the outbreak.