My several hundred page site filled with guide quality how-to articles with hundreds of "thank you" and other constructive comments, dating back to 2005, was smacked with a 50% traffic loss. It seems that the 12 pages which contain an affiliate link(which is clearly labeled) suffered a 95% drop to go along with the sitewide drop.
There is DEFINITELY and anti-affiliate feel to the latest changes. I'm not removing the pages, or the affiliate links. They make sense on this site and what I'm replaced with makes Google look bad. /shrug.