In the book, The Great War, it is made a point that the Imperial forces stationed in these two counties had been destroyed when the Aldmeri Dominion launched its devestating suprise attack against the Empire. What forces had been being referenced? Had it been the County militas and guards, or did they station a legion(s) there as well?

We know that three legions had been completely destroyed during the war, with the remaining suffering at least 50% loses as well. However, I only know of one of them by name, the 8th who acted as a rearguard for the Imperial forces escaping the capital city. As far as I remember, no other instances had been mentioned of a legion being destroyed, and the only times it could have happened would be during the March of Thirst, and the flanking of the Bravil-Leyawiin defences.

I would guess that given that the Empire and the dominion were pretty much at a cold war before the Great war, I would assume that much of The Legion is stationed at the border between Cyrodill, and Valenwood/Elsweyre. So there might have been atleast one Legion that might have been destroyed there.