Well the 2011 PDF on the WH website was taken down after six hours or so [I am going from memory, is that correct?],
and replaced with a flattened PDF file with all the layers concreted into one.
If the layers were not evidence and innocent, why flatten the PDF layers in the new version and replace the file on the WH website?
I think that might tend to indicate a “Mens rea” at work.
I think it was around 3 hours later, IIRC. By then the damage was already done; I think a lot of people woke up in those few hours. Not enough, but even some Obama voters who know something about computer files.
I just this minute downloaded the White House pdf and opened it in Adobe Illustrator and it still breaks up into the 9 layers.
http://www.whitehouse.gov/sites/default/files/rss_viewer/birth-certificate-long-form.pdf