Highlights from DEVONthink are embedded in pdf

I’m using DEVONthink to index my folder of research articles, organized by Mendeley. This works great except for a few things.

  1. Any highlights I do from DEVONthink are embedded in the pdf and cannot be edited in Skim, and are not included when I want to export highlights from Skim.

  2. Highlights that were made and were editable before indexed by DEVONthink have also become embedded.

  3. When I move a pdf out of the indexed group (that is, INSIDE of DEVONthink, e.g. from the database inbox to a an other group in the same database) I can’t add any highlights to it anymore. The highlighting button is greyed out.

Is there some settings to be tweaked to solve these problems? Or is this one of the cons of indexing documents instead of importing?


Indexing vs. importing is not a factor here.

Skim does not read annotations created in DEVONthink (or Acrobat, PDFPenPro, or almost anything else) until you convert the PDF annotations to Skim annotations. Skim > File > Convert Notes. You’ll see this dialog open:

Of course, once you have converted standard PDF annotations to Skim annotations, then it’s Skim you need to use for editing your annotations. (There are workarounds; they are not pleasant.) Skim is great, but it does not play well with the rest of the PDF universe.