atlrus - 12:12 pm on Nov 12, 2012 (gmt 0)
Is it possible that somebody entered a DMCA against the site because the content had been plagiarized? I know this happens a lot in web design and logo design.
This is the first thing that popped into my head when I read the OP's first post. It's the only time I've heard Google actually de-indexing a site (besides self inflicted de-indexing, of course).
You were clearly told that the site was disabled in Google Search, so nothing technical here - someone at Google just removed the website manually.
I have never had to deal with DMCA, but I am sure there must be a way to check on this.