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I removed a whole section from the site at the same time. Webmaster Tools shows the incoming links for every page in the section as other pages in that section. It's a whole loop of pages linking to each other and generating inbound links even though they all no longer exist and haven't for many months.

Yeah, Webmasters is reaally slow to update. Thankfully they offered a way to delete old pages. If they come back though, then it should show the source of the link.

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