tedster - 7:28 pm on Sep 18, 2012 (gmt 0)
I've seen behavior like this once in a rare while when it wasn't a penalty. The disappearance hit fast during a significant update, and then it quickly changed back. I do have some strong ideas about what kind of bug this might be, but there's little we can do about a short term bug so my theories are pretty irrelevant.
Penalties don't usually (don't ever?) last 3-4 days. I think you've been hit by a Google data bug. Please do keep us all updated about any changes for the subdomains.
BTW, if I'm right about this particular bug, it could mean that
your site is flagged as a STRONG one, not a troubled one.