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I never knew until a year or so after the event about Google deciding that links out to the affiliate site had to be rel="nofollow" (there are probably many thousands of site owners who don't belong to forums who still don't know that).
There are two affiliate merchants I was no longer willing to partner with so I removed all my links to their product pages. But GWT says there are hundreds of merchant links still in existence to my site like:
I have asked the merchant to delete/404/no follow these links, which they have not done and instead they are redirecting the 404 event to their home page.