The problem is, games use more than just the immediate files in that folder. Information about the game is inside your registry, including information about its version. If you were to try to update it, the updater wouldn't even know you had a copy of Rome or Medieval installed in the first place.
*** Personal experience.

***
Anyway, I would just bite the bullet and install again. If you look in your C:\Program Files\Activision\Rome Total War folder (I think it is Activision), you can find the folders you want. Just copy the "Saves" folder to a CD or flash drive, and in a few hours of reinstalling windows, and reinstalling your games you should be fine.
I should know, my new computer is sitting unused because I messed up my partitions. I decided it was a good chance to get Vista and ordered it, but until it gets here my drive is basically empty.