I have symbolic links set up, too, so the 4 WoW folders on my computer (C:\games\wow, F:\games\wow1, F:\games\wow2, and F:\games\wow3) all share 1 Data folder (G:\games\wow\data). I have Addons shared, too, so updating the addons in one automatically updates the others.

Anyway, the Patcher also updates files in the Base installation directory: for me, my C:\games\wow. I simply copied all the files in that folder to the other 3, and it works fine now.