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One of the functions of the Kobo Utilities plugin is to take a backup of the database if it's not corrupted.
Take a look at the Kobo Utilities Customize Plugin menu, especially the Devices tab. On it you should see options for Device Database Backup, where you can select either Backup the device database daily which will take a backup once a day, or Backup the device database on each connection which will take a backup each time the device is connected.
Also set a larger number for the Copies to keep option.
Be aware that the database gets updated when you disconnect the device from your computer, so if you want to load books in small quantities you need to send to device, then disconnect the device, wait for the Kobo to complete the Processing function and then reconnect the device and send more books.
There are no issues with the f/w; trust me when I say that if there were issues, either davidfor or myself would have ensured that the issue was prominently displayed in these forums, and that we would have worked with Kobo to get the issues resolved ASAP.
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