I was using the sync function also when I first got my PRS 600 reader. I worked great for 2 days then started hanging. It worked when it wanted to for me. Do yourself a favor and use calibre instead.
Calibre is super easy to setup, operate, and transfer your books to your reader with.
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I know that this doesnt answer your question, but the honest truth is I dont think their is an answer. Sony sync simply sucks stupendously.
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