attached is the script i created for this (this is the exact same one that is posted in a code block at the rts.net forum). then, you can run:
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sh wrf-fix --no-replace /path-to-wz-files/*.wz
obviously replacing path-to-wz-files with the path to your warzone files. any number of .wz files can be listed here, and they will get batch processed. after it processes them, you should have a directory that would match /tmp/wrf-fix.*, or it might be somewhere else, depending on how mktemp works on your system, or depending on your environment vars -- at this point, you can mv the .wz files residing in that directory back into /path-to-wz-files/. note, this assumes you have zip, unzip, mktemp, and sed as available commands.
now, while leaving out the --no-replace option would do that work for you, it would probably require elevated privledges, and, while i can tell you the script isn't malicious, it's always possible there's some nasty bug, and even in the interest of security, it's easier to mv the files yourself then it is to look over the script and make sure it won't do anything bad.
oh, and while dev did suggest an improved method for handling the downcasing operation, i'm too lazy to implement it since you're the first person to mention this problem in some time, and the result is exactly the same (just in my case, a little slower).
in regards to your point that lowercasing the references in the .wrf didn't work, well i didn't just lowercase those references, i downcased *all* of them, so it might be that. also, this requires that all the filenames themselves are lowercase, but i believe that had already been done a few releases ago. further, it seems to me that there is some bug out there that causes the exact same problem with that mission, but for unknown reasons -- at least, that's what i've been able to guess from some other posts on the same problem, so it is possible that you could be afflicted with both the wrf problem and that bug, if such a bug really does exist.