The notes from the Sonys can be exported to your computer with the included software. If I remember correctly, this will give you a file with your typed and handwritten notes, as well as the first 100 characters of each highlighted selection. (Actually, it looks like that's 100 characters for DRM-protected, which would include library books, and 2,000 characters for non-DRM protected material.)
I would guess that if you export your notes to your computer before the library book is due, you should be able to save them since it creates a separate file. I don't have any library books to test, though.
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