Came accross a saimialr situation when we updated to 5.4 - I had to manually update them all to the latest version, did it all via SSH so it was faster at least
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I once upgraded a few installations on the same server. I put the zip file in one directory, unzipped it, then used a shell script to cp the files to each of my virtual domain subdirectories in turn. Of course, I still had to go to each site to run the installer, but at least it saved all the uploading and moving of files needed. I'm sorry, this was years ago so I don't remember what the shell script looked like.
