Not sure exactly what you're saying, but the patch semi-killed my warcraft install. Specifically, it deleted my junction point (I use Windows XP x64).

I have 5 instances of WoW, each on a separate drive, and use a separate SSD for the Data folder which is junction-linked to all 5 instances.

I ran the update on one copy of WoW, which appeared to succeed fine. On running WoW.exe, I got an error message however about an MPQ file. Repair.exe told me my install needed to be reverted first, then gave me the good news that I would need to reinstall.

Fortunately I checked the contents of the WoW folder and noticed that the Data folder was gone. It was still present on the SSD drive, so I just re-junctioned and everything started to work OK.

After that I was able to do my usual copy of all folder contents except Interface, WTF, and Data from the patched WoW folder to the other 4 and I'm back in business with 3.0.8 up.

I suspect it might have something to do with renaming/moving of the Data folder as part of the patch. Or possibily it was just an idiosyncratic thing on my PC.