opening up previously hidden content

As a favor to a friend i helped them out with some SEO work on their site.

They had a bucket load of content hidden in flash.

The site is about 3 years old and the front page ranks well for a competitive phrase.

We opened up their content using simple html pages and a good sitemap.

Within a week google ate up most of the pages and traffic went through the roof.

But last week every page (including the front page which previously ranked) went MIA from the Google index.

They can't be found using site: or searching for exact/unique phrases in the content.

Have I nuked this site or will it pop back up?

and getting nuked by Google