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If you use send-to-kindle, such that annotations get saved to your account's cloud storage, then you can export the notes. But you have to use a tablet (Fire, iOS, Android) Kindle app. If you export as email attachment it will be an .html file, with Android/Fire you can send to any app registered as a Sharing target.
The Kindle uses a cloud service to send PDF+CSV files as attachments to your Amazon email address. The annotations have to be in the cloud as well. Side loaded book annotations are only stored locally.
With the tablet apps, it converts the annotations on the device and so it does not go through the cloud service. If you side load to the tablet apps, it probably can export those annotations. But I have not tried it.
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