Yes, there do appear to be some 2010 updates to the documentation, but the original AT91FR40162 was obsolete as far back as 2005. In conversations with ATMEL they have steered me away from any part which integrates a separate flash die (ie AT91x40 series). This is because the flash die kept getting shrunk, and the whole CPU+Flash would need to be requalified. My guess is some very important customers use some of these older parts, perhaps military or automotive. I would definately check if you can source/purchase these parts, and what long term availability will be. There are better, fast, cheaper parts in 2012.
http://www.keil.com/dd/chip/3522.htm
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