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If you're using calibre, you just need to point it to where Sony has stored the books. Add books (pick the one to add from directories, including subdirectories, multiple books), then go to the folder Sony stores it in. Under Windows 7 you're looking at documents/my books/reader. Not sure where it is under other OS's.
I had a bookworld membership that migrated to Kobo last year. Most people were set up no problems, but because I had accounts with both already and they were both linked to the same email it didn't go through automatically. A single support ticket fixed the issue (to bookworld) so you may want to open a ticket with Sony beforehand giving your Kobo login email (NOT the password, of course). Or, you could try pre-empting it by contacting kobo support. They've always been great, although a little slow to reply at times, in any issues I've had.
I love both Calibre and Kobo. Never use Sony Reader except to download DRM books in the first instance, after which I pull them into Calibre. In Calibre, too, you can search for a book you're looking for and it pulls it up in a whole range of sites, so you can compare prices and get the best deal. I'm always using that feature.
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