How exactly did the Red Queen know the exact number of people still alive on the planet and how could she guarantee they would be extinct when the countdown reached zero? e.g. What happened to the armoured tank that left with the survivors and children, and the kung fu guy who was being dragged behind? Did they survive the countdown? Was it really a bluff to get Alice back to the Hive?
It isn't a great plot, you have to take a bunch of things on faith that don't really hold up if you think about them too long. But. Basically it's this:
Umbrella is laying siege to all the remaining human camps - like the one in Raccoon City. They are going to all of them with tanks and armies of zombies in order to destroy them.
Plus, each human settlement has at least one traitor inside, helping Umbrella/feeding them information.
Plus, at least some satellites are still operational and under Umbrella control because we see them throughout the film when Alice is being tracked by The Red Queen/Wesker.
So... all those things combined, supposedly, that's how the Red Queen knows how many there are, and that in 48 hours they will be dead.
As for what happened to the settlements: The Red Queen says at the end of the film, after Alice killed Isaacs, she called off the attacks just in time to save the settlements.
As for the Raccoon tank with the dude: that guy was evil, they probably let him run until he bled out/got tried and he was eaten. Then they went home. Does it really matter?
Take moments of happiness where you can; the world will take the rest.
It also raises the question - in the tank, Issac's tell the commander to turn back, but he refuses and says "I can't sir, I have my orders".
Considering at that point, Issac's doesn't know he's a clone and believes to be in charge of Umbrella, with Wesker beneath him, where are these supposed orders coming from?!
Another little plot hole - not the worst but silly all the same.
Also it means at the end of the movie there are still lots of umbrella forces and bases left around the globe.
'The Final Chapter' - for Alice, maybe, but not for the Anderson franchise, still stories to be told there about this universe.
Satellite
shareHumans are not computers to shut down a specific second so it doesn't make a ton of sense, but presumably Umbrella's schedule was for their final attacks to commence in 48 hours (yes, precisely 48 hours from that time Red Queen contacted Alice, what a coincidence!!11) and the last humans would die within minutes.
As for how does she know how many humans are alive, Umbrella still have their satellites.