If you edit the file "Kobo eReader.conf" on your Kobo, you can add these lines, and an option to export ALL the highlights in a ebook to a SINGLE file will be added to the readers Annotation menu:
Code:
[FeatureSettings]
ExportHighlights=true
If the line "[FeatureSettings]" already exists, don't add it again, just put the "ExportHighlights=true" line beneath it; if it doesn't exist, add both lines.