Rank gone over-night

I have been doing travel agency website, for a localized market it was general domain but still was pointed out in the webmaster tools that the domain is for a specific language. Everything was fine completely white hat seo done to the site, few links here and there and posts were ranking well on google for specific terms which was the point.
I have also made few specific sites for example for Greece and there were links pointing to main domain, suddenly last night all rankings for main domain have dropped out, the site is still indexed by google when i check google main domain is still there.. posts, everything else.

I have used link detox tool and it said that links from new sites were a problem, i have added disallow for those new domains and removed links from them that pointed to my website. I have pinged the site, and submitted the re-submition index for the main domain.
the only strange thing that i see in webmaster tools is this
on index page there is only 3 links indexed !?
and on the sitemap there are 185/186 links indexed.

Anyone had similar problem, i guess i caught some penalty.. Can site recover it's rankings or not and in what time frame. Or should i change the domain on the site to something new will this affect the penalty or, start completely new website? s

I had a similar thing happen before. Are you using adsense on the site? I changed the location of my ads, i had all 3 above the fold, so i moved them around. The rankings all went back up about 4 days later.

Try to check your url in Google. Is the url still on Google or not? If the url is still on Google, your url is not get penalized. Try to rank it back.

I think that you don't need to move to a new domain. You only fix your current website. Use http://www.google.com/webmasters/tools/‎ to analysis your website.

everything i try to write on this topic, i get warning that, it's not allowed to post .. :S

There are no ads on the site as it's informative