You don't update anything. The whole final version of the game is in the package from the store downloads page. I suspect the prompt you got when doing it again was just due to extracting it in the same location as you did the first time.
You can just run the copy you extracted in the location you extracted it, and toss your old copy.
Ok. Just to be sure I understand. The download was am entire GalCiv II game with the updates, not just the updates? I ask because what I did was get updates, not the whole game. It was a 1.18G download.