For the record, the Eugenics Wars duology by Greg Cox establishes that Khan seized power covertly in most of Asia. The governments nominally stayed in place, but he had them sufficiently blackmailed that they all kowtowed to his whims. Most of the civilian populace in Asia were aware of Khan's unofficial control, but the general populace in the West remained ignorant of his influence until after the Eugenics Wars -- which Cox postulates as consisting of the large series of post-Cold War brushfire wars that mostly went ignored in the U.S. -- were over. Which is not all that unrealistic when you consider that most people in the West are ignorant of, for instance, the horrific wars in Central Africa in the past thirty years.
Those were good books, but unfortunately they would only work now if you ignored the lines in ENT about the 30-35 million death toll, Archer's great, great grandfather fighting in North Africa during the conflict (To the best of my knowledge, nothing really happened around that area in the books), and the Augments in the midst of growing thousands of Augment embryos whereas in the books I don't think they were anywhere near to doing that.
I don't think that's true at all. For one thing, the books had a huge death toll -- it's just that the deaths were perceived in the U.S. as being the result of brushfire wars rather than part of a larger pattern. (And the idea that that many deaths could go unnoticed in the U.S. isn't that unrealistic when you consider that 4 million people have died in the Second Congolese War without most in the U.S. really noticing; American ethnocentrism can blind people to a lot of things.)
And Cox's books also referred to the U.S. Armed Forces as eventually getting involved; there's nothing inconsistent there with the idea of Archer's great-grandfather fighting with them in Northern Africa. (Also, bear in mind that there's no particular reason to presume that Archer's great-grandfather was fighting for the U.S. military in the Eugenics Wars.)
I don't think the Cox books ever established anything one way or the other about whether or not the Augments were in the midst of growing future Augment embryos.