I'd also like to add a side note. After trying to log in and botching the installation because one of my clones hit it, I had to do some manual stuff to get the files back in order. Since this didn't complete correctly, every time I tried to patch my primary instance (the one all my other instances "junction" off of) it would fail mid-way because it thought the versions were out of whack.

After some inspection, the Data folder, and the subsequent localization folder (for me, enUS) had a couple of patch-2.MPQ files I had to remove. After that, it was no longer confused about the versioning and the update went through as expected.

Now I'm back up and running, all is well.

[Edit] I seem to have a problem with opening my mouth too soon. I also had to copy over the executable file, which seems abnormal to me. Even though all of my data comes from the same instance, my clones kept prompting to update. I notice the .exe file had been last modified today, so I copied it over and now that seems to have fixed it. Strange. [/Edit]