Here’s how to make Calibre OCR play nice with Devonthink. If you bring a PDF file created in calibre into Devonthink and then highlight something, the annotation often comes out as gibberish. It seems the trick is the change your preferences in Calibre: go to Preferences…Common Options…Look & Feel. Put check marks in two boxes: Embed All Fonts in Document, and Subset All Embedded Fonts. Click Apply.
OCR should now work in Devonthink.