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That all looks perfectly fine - which means the plugin upgrade worked as expected and put the data in your database. The library preferences stuff is just the underlying data behind your list settings - the long lists of numbers are the calibre book ids on that list, so it is showing you have at a rough guess around 100 books or on that list.
Perhaps your device has changed. Have you reformatted it for instance? That will result in the device getting a different calibre id, which will mean that list is no longer associated with your Sony. With the device plugged in go to the Devices tab of this plugin and look to see whether the Status column shows your device is conencted, or whether that column is blank and "Add connected device" is enabled. If so do the add, delete the old device, and change your list to point to the new device.
The other suggestion is to run calibre in debug mode (with your device disconnected), then plug your device in and post the output in a spoiler tag. The stuff that is of interest will start 'READING LIST:' in the debug output.
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