Sorry I should have addressed this as part of my tip. I am afraid there is no clean and easy way around this. I tend not to use the authconfig command (or the associated GUI) to configure systems. But if I have to run authconfig, I make copies of the system-auth file before running authconfig. That way I can add back in previous changes made to the file.
I also recommend the use of a central configuration manager like cfengine or puppet to keep files like this up to date from a central point.
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