Since this thread was dug up from the past, i'll give my update as I still still use symlink'ing and find it quite effective without any of the issues that Mukade describes.
If you're using symlinks, the trick with the 4.0.1 patch is having the WoW.mfil and WoW.tfil symlinked as that files get exclusively locked by your first instance, and the others won't attempt to download content on the fly. This is what causes the crash.
I've installed WoW on my SSD ( d: ), and created a "Multiboxing" directory. Underneath that, I have five subdirectories "a", "b", "c", "d", & "e", and copied the following batch file into each one. This will recreate all the subdirectories and symlink whatever needs linked. I've only used this in windows 7, so use at your own risk.
mklink /d Data "D:\World of Warcraft\Data"
mklink /d Cache "D:\World of Warcraft\Cache"
md Errors
mklink /d Interface "D:\World of Warcraft\Interface"
md Logs
md WTF
mklink "BackgroundDownloader.exe" "D:\World of Warcraft\BackgroundDownloader.exe"
mklink "Burning Crusade Install Log.html" "D:\World of Warcraft\Burning Crusade Install Log.html"
mklink "dbghelp.dll" "D:\World of Warcraft\dbghelp.dll"
mklink "DivxDecoder.dll" "D:\World of Warcraft\DivxDecoder.dll"
mklink "ijl15.dll" "D:\World of Warcraft\ijl15.dll"
copy "D:\World of Warcraft\Launcher.exe" Launcher.exe
copy "D:\World of Warcraft\Wow.exe" Wow.exe
copy "D:\World of Warcraft\Scan.dll" Scan.dll
mklink "Patch.html" "D:\World of Warcraft\Patch.html"
mklink "Patch.txt" "D:\World of Warcraft\Patch.txt"
mklink "realmlist.wtf" "D:\World of Warcraft\realmlist.wtf"
mklink "Repair.exe" "D:\World of Warcraft\Repair.exe"
mklink "unicows.dll" "D:\World of Warcraft\unicows.dll"
mklink "World of Warcraft Install Log.html" "D:\World of Warcraft\World of Warcraft Install Log.html"
mklink "WowError.exe" "D:\World of Warcraft\WowError.exe"
mklink "Scan.dll" "D:\World of Warcraft\Scan.dll"
mklink "Battle.net.dll" "D:\World of Warcraft\Battle.net.dll"
mklink "WoW.mfil" "D:\World of Warcraft\WoW.mfil"
mklink "WoW.tfil" "D:\World of Warcraft\WoW.tfil"
What I like about this setup is that you retain your own WTF directory for saving customized settings for each toon, and when I play solo, I'm playing from the main directory which has all the graphics maxed.
Before I log on to multibox, I always hit the launcher and see if there's an update, if an update is there, I let it do it's thing then re-run my batch file, otherwise, I simply close to launcher and start everything up with my broadcasting software.
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