Wildcard Subdomain DNS SEO Oops! Duplicate Content Smack From Google?

Ok so I have a .com EMD that is over 6 years old and been #1 for many terms for some time ... I within the last couple weeks switched the site totally from using 100's of subdomains to simple sub-directories to make life easier for my crew and the public. I then implemented wildcard dns for the subdomains only problem with that was that if you went to example.example.com it would go to the home page example.com but would show example.example.com in the address bar. Well yesterday my site basically disappeared from Gsearches, it is still indexed but no where to be found under my terms anymore. I am assuming that the site was dinged for the dreaded duplicate content as the subdomains where showing the subdomain address in the address bar even though they where on the main index page of the site. Anyways that issue has now been fixed via the .htaccess file and now when someone goes to one of my subdomains it shows the index page url in the address bar now instead of the subdomain url. My question is do you believe this is why Goog kicked me in the nutts and if so how long do you think it would take to bounce back from that mistake?

Cheers Mates!

It could take a long time to bounce back. I have heard stories of people doing UI updates and structural changes to their sites, being sent back to page 3, and then taking up to 2-3 weeks to get back to normal. I have also heard stories of people never quite getting to what they had before, but the bounce back is usually 2-3 weeks.

I heard it takes some time, probably around 1 month for you to bounce back to (hopefully) the top.