I lost basically all of my sites in the last 2 days. Heart-breaking at minimum. No interlinking. Only thing would be I just moved servers, and just switched to a different webmaster tools account.
Not sure if it's the case with you, but I noticed a drop in traffic for a few weeks after I moved my sites to a new server in a different state/IP address, but it did go back to normal eventually.
It is not a point of recovering positions. I mean my site IS NOT INDEXED. as in... site:mydomain.com brings NO results.
I posted about this a few days ago right here: http://forums.digitalpoint.com/showthread.php?t=1277676 in which I relayed that all my sites that I listed in Webmaster Tools were de-indexed but the few sites that I never got around to are still indexed. It is disheartening at first but you just go back and keep working it because what are you going to do?
Did the domain names or the URL structures change? If they didn't then my guess is that moving a lot of sites from one IP to another raised a red flag with Google. Then you got a manual review which resulted in deindexing. Usually Google won't completely deindex a site unless they think your are doing something black hat or provide no value at all to the internet. Take a objective look at your sites and decide if they add value to the internet. Also look at any linking practices you have and see if you've run afoul of Google's quality guidelines. About the only thing you can do at this point is to clean up your sites then file a reconsideration request with Google.
Same thing happened to me in Jan/ Feb. From 3500 pages in the main index, I dropped to 0. Didn't know what to do except wait. Fortunately I'm now recovering to about half the daily traffic I used to have.