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I tried two methods:
1) Adding the config setting for exportHighlights=True. This adds a menu option to to export highlights. It worked ... except the highlights were truncated if they were more than a 140 characters are so.
2) I switched to solely using KOReader. While looking at how best to integrate KOReader with Calibre I found the KOReader Sync plugin. This plugin allows you to sync highlights, bookmarks, annotations, reading progress, reading status, and more into custom metadata fields in Calibre.
I decided to stick with the second option as I've really been enjoying KOReader for my sideloaded epubs.
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