If you're using Symbolic Links, the only safe route I've found is:

a) Structure it so you have:

Parent WoW (Patch this)
-- Symlink 1, run WoW here.
-- Symlink 2, run wow here.
-- etc.

b) Break the symbolic links.

c) Patch Parent WoW.

d) Re-Symbolic Link from the now patched parent wow, to each copy.

e) Copy the wow.exe and launcher.exe from the patched directory to each of the symbolic link folders.

Personally I noticed a very slight performance improvement with the symbolic links, namely the loading times overall.

However, for me the only big advantage is having different graphic settings for each of the wow copies. I had the ability for 5 copies of wow, with boxing, each at very low settings. And then a sixth wow, from another symbolic link folder with all of the eye candy on, for solo pvp/raids which do not challenge my system.

I've gone back to a single wow folder, running everything on minimal settings; twice with Symbolic Links I've had errors which the GM in the tech forum basically said, reinstall the game is the only option. It's certainly easier to run just one installation of warcraft, but that's your choice.

Currently wow is kind of bleh; basically just playing the auction house game at the moment, and chatting with friends here and there.