I have taken a look at all of our sites top to bottom (600+) as we are a high-end affiliate company. While we have a few that have the symptoms outlined here, the majority have remain unchanged or have improved. It should be stated that our sites are not MFA or thin affiliate sites. Typically, our sites get confused with the merchant's site as we product better sites than the merchant. It is just how we do things.
Most of our affiliate sites are PR5-6 and have a very strong back link profile in the 200k-800k range. I see no similarities between the sites that tanked and those that didn't. I wish I could lend more info to the forum here but right now I have more questions than answers as to what to do from here in terms of the sites that tanked.