It's happened to me also Skuba. One of my sites has 200k+ pages and over 4K backlinks. It's bad enough that G only shows less than 250 backlinks right now, but the vast majority of the pages (90%+) have gone missing. On April 2 our daily traffic dropped from an average of 30K visitors per day to next to nothing. We have no connection at all to Amazon, so I suspect that it is in fact a filter that demands a certain level of difference between pages or else it blows them away.
But this is one of the thing I wonder. It needs to have a difference between our content and some other site content or a difference between our pages?
If the second is true, it's not very fair considering that most sites (specially ecommerce) have very similar pages, just changing the products offered in each page. This is actually true to even content sites.