Under those circumstances, I think depending on just when they got the wakeup call, the Project teams might very well be tasked with re-establishing the human population on the planet and not just re-establishing one particular country.
That would require many of the elements already present in the Project as we know them from canon material but probably also some serious adjustments to take account of other needed activities. These would be such things as bolstering the survival rates of extent human populations, increasing birthrates, reducing infant mortality, establishing 'needed resource' (e.g. food, water, tools) production, increasing education about health and so on.
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