I'm not quite sure that this is what you are looking for, but Windows environment variables can be changed (taking into account Windows 7): Control Panel → System and Security → System → Advanced System Settings → Environment Variables (button).
On this screen, you can set user variables as well as system variables. Perhaps the settings that you want to find in your application are stored under the user, and not in the system, and then open the application under another user so that these variables are not available?
Create the variables you need as system variables solve your problem?
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