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Yes, you can definitely put books in a folder that the Kindle will not see. If you use MobiPocket 6.1 to send mobi files to the Kindle they will be put into a folder called ebooks. The Kindle doesn't "see" this folder so the files have to be moved by you while the Kindle and/or the SD card is connected to your computer.
The Kindle has a "Content Manager" that allows you to move files back and forth between Kindle memory and SD memory. But the content manager will not see any folders except the default folders so storing books in a different folder requires you to connect the Kindle to your computer to move them into the document folder.
So it won't work exactly how you want but it is doable as long as you connect to a computer.
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