As "Rizla" mentioned "it depends on the OP's requirements", and his workflow. For instance, while Koreader has no notation function, Evernote has. Once you open the "Koreader" notebook in the Evernote program on your PC, where your highlights are, you can add all the notes you want.
It is also possible that the Koreader "Progress Sync" would include the highlights, given the way it appears to work. (I haven't tried progress syncing a highlighted ebook, though.)
Luck;
Ken
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