There are ways to get the annotations or highlights from some devices and apps. I look after a plugin for calibre that can get them from Kobo, Kindle and tolino devices and put them in the metadata in calibre. It can also get it from some apps, but, others could be added. There are other methods that work in different ways. One I've seen recently gets them from Kindles via the your Amazon page. I don't look at the other devices enough to know what other tools are out there, but, I know they do exist.
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