Top Paper
1 ---------
Gap Tray
2 ---------
Bottom Paper
Paper would be collected from bottom using standard scanner/paper style paper grabbing, scanned or printed to and placed in Gap Tray. Gap tray and entire top paper stack need lifted and placed back on support layer 1.Pages would probably be upside down of their original unless they were fed back and forth.
All the paper would need lifted up, so there would be a limit, unless... a different idea would be the same thing along a horizontal track of papers.
I'm still liking the idea of a scanner shredder. http://designforpeople.ca/?p=215
To extend this stack design make it like an inverted shredder with a 5" shop vac hose connected to the top :P