I think you are missing a lot of the problems. Ignoring the massive losses of people due to the Project's absence, the Project was depending on the knowledge and resources available immediately after the war, and without those resources the Project will see a lot of people suffer or die that otherwise could have been saved.
Worse, the intervening century and a half has given despots like the Rich Five and Krell time to entrench themselves and flourish, meaning that an organization designed to bring order out of chaos must now also serve as an insurgency. The Project can still defeat them (presumably) but again, how many more (Project and civilian) will be lost?
The Project has lost both it's leadership and a decent chunk of its membership, and has awoken into a world vastly different than the one they were expecting with challenges that are both far greater and different in nature compared to their original mission. Given that the Project's remaining resources are never spelled out, it really is not possible to know whether or not they will be able to succeed or even survive.
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