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If one uses calibre I'd do it in a few phases. First of all use Kobo Utilities to save reading location of all books on the old device. Then either using the command line or a graphical file manager copy the folder along with any sub folders where your books are stored on the old device to your computer's hard drive.
Disconnect the old Kobo.
Attach the new Kobo.
Copy the directory structure to the new Kobo. (Note that you do not want to copy the .kobo folder).
Disconnect the new Kobo and let it import all the content. Finally reconnect the Kobo and use Kobo Utilities to restore reading location .
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