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Using Kobo Utilities you select an ebook when Kobo connected and select Copy Annotation and it opens a window. You then copy/paste to a text editor (Notepad++ in Windows or WINE, KATE or similar in Linux), and then you can save a file.
The Annotations plugin copies the annotation into Calibre's book record.
I've used the Kobo Utilities method maybe over 1000 times with no issue except once when Kobo database was corrupt. The Kobo Utilities method by default doesn't directly create a file or add the data to Calibre.
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