Software Update completely wiped out computer

I clicked on automatic software updates before I went to bed the other night, and now my screen only display the set-up assistant, much like I had just installed Leopard. But, even following the prompts, I am stuck in a loop in set-up assistant. I am afraid to re-install because I am afraid it will wipe my hard drive out. Any advice?

Follow these Apple instructions:
http://docs.info.apple.com/article.html?artnum=306998

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