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Calibre is best for getting annotations out. If you use it you don't need the config menu option to export, otherwise it's handy.
The most I've done is about 980 in one book. I use the Kobo Utilities in Calibre (David's good work), or Annotations in Calibre for a Kindle. I copy/paste the Kobo Utilities "Get Annotation" into a text file where I reformat it for my needs.
The Kobo Annotation support is fine on the device.
You can also use a WP to make a document like a diary, use Calibre to make it into an epub and then add notes.
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