You can use both. From the Calibre FAQ at
http://calibre-ebook.com/user_manual...nage-my-reader
Quote:
Can I use both calibre and the SONY software to manage my reader?¶
Yes, you can use both, provided you do not run them at the same time. That is, you should use the following sequence: Connect reader->Use one of the programs->Disconnect reader. Reconnect reader->Use the other program->disconnect reader.
The underlying reason is that the Reader uses a single file to keep track of ‘meta’ information, such as collections, and this is written to by both calibre and the Sony software when either updates something on the Reader. The file will be saved when the Reader is (safely) disconnected, so using one or the other is safe if there’s a disconnection between them, but if you’re not the type to remember this, then the simple answer is to stick to one or the other for the transfer and just export/import from/to the other via the computers hard disk.
If you do need to reset your metadata due to problems caused by using both at the same time, then just delete the media.xml file on the Reader using your PC’s file explorer and it will be recreated after disconnection.
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Hope this helps!