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I wrote a script last weekend, but put off uploading it because I wanted to include a version of find for the older 3XX ereader models. However, I'm not sure that the notes are in the same format on those devices, so I think I'll just release the script for the Pro models only.
The script deletes all the state data and notes for ebooks that aren't on the device any longer. To make the script simpler, I used find and bash, and included them in the zip file.
As you noted, deleting the notes may not be what is wanted. However, making the script interactive would make it tedious to use. If you want to save notes, I think it's better to just comment out the notes handling stuff in the script, and just use the Notes application to delete unwanted notes.
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