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If using Calibre "Kobo Utilities", then any Kobo with the current or last few years firmware is better than Kindle, Nook or Sony for taking notes / annotations and getting them into something else.
If you want random notes, then use a wordprocessor -> docx -> Calibre -> epub and make an ebook with A - Z, Topics and Dates as headings and a bit of body text (maybe multiple lines) to add annotations to.
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