Nope, done within a couple of hours - see timestamps above. We repeated the process twice, and I can't believe anything happened to the XML files. I literally saved the request one and uploaded it, without even opening. I'll check with the customer, but he seems pretty clued up and has no reason to touch the file!
Being a corporate server, is there a chance you're trying to save out any files that are part of the protection system into a location they don't have access to, or anything like that?