I agree that it is a somewhat bizarre oversight, if oversight it was. If it was intentional, it's shocking that more of an explanation wasn't offered in HW. I also agree that a returning federal troops -> local/regional militia balancing of the books could be a partial solution to the irregularities in numbers.
That said, I think that you tend to look at things very much by-the-numbers, and fail to adequately consider or account for the human factor in all of this. Civil War vets didn't have to fight- away from home- for four or more years. Neither did WWII vets. Even in our longest wars, Vietnam and The War on Terror, the majority of vets didn't have to be away from home continuously for more than 12 or 13 months at a stretch. To expect nearly every returning soldier to stay in uniform, follow orders, and not go home (i.e. desert) at the first or second opportunity, is almost as unrealistic as the disappearance of so much returning NorthAg and CentAg strength.
Another solution to the conundrum of the "missing thousands" is that HW simply didn't count troops still on furlough. This doesn't account for the missing whole units, but it could explain why the total numbers of troops in CONUS post OMEGA are so dramatically skewed.
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