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This from Calibre FAQ:
I used calibre to transfer some books to my reader, and now the SONY software hangs every time I connect the reader?¶
You should not use both calibre and Connect to transfer books to the reader. You can fix this problem by:
* Removing any storage cards from your reader.
* Deleting the file media.xml from the reader’s main memory using windows explorer (search for the file to find all locations where it is present). Note that by doing this you will lose all your collections, bookmarks, history etc.
* Unplugging the reader and waiting till the list of books shows up again
* Re-connecting the reader and starting the SONY software
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