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Consider not using the sync function. When I first got my Sony Reader and Sony's library software, I quickly found that the sync function was more trouble than not, especially since I was also using calibre to upload books and conflicts happened.
Now I never use Sony software's sync function. You can manually transfer files from your computer to your reader by highlighting the books you want to transfer and then dragging them (by using the left mouse button) to the Sony reader icon that appears in the Sony software desktop when you plug in your reader to the computer.
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