Amazing advice! I use a Kobo reader because it can be used without registration (do a quick search engine search on how to do this), and I transfer my epub books via usb using rsync. Turns out you can edit the Kobo's config file and turn on a feature that will export your highlights and annotations to a text file on the Kobo's root:
https://www.reddit.com/r/kobo/comments/7swz6v/exporting_high...
I never would have thought to look this up without reading your comment. Absolute game changer. Cheers!