The Highlights app, v1.5, out today in the Mac App Store, has a feature that will export annotations that were made on a document stored in your DEVONthink database using DEVONthink links (reference URLs – x-devonthink-item:// ) instead of highlights:// links.
This was a point for some readers here with the last release of Highlights.
Note: to make this feature work, you need to install a helper script in Highlights > Preferences > Export, and you have to export to DEVONthink using the command in the menu: File > Export To > DEVONthink. Do not expect the DEVONthink Share menu widget to export from Highlights with DEVONthink links.
(The technique Jonas is using here with the helper script is interesting and clever, if you’re interesting in scripting. The Highlights helper script searches for the document in your database and, if found, it grabs the UUID of that record so that Highlights can build the links. It’s a technique other developers could use to build helper apps that integrate with your database records.)