You could select the files you want to move to Finder and drag them into a folder in Finder, and then index that folder.
Or, slightly faster, you could create an empty folder in Finder, index that folder, go back to DEVONthink and drag the PDFs into that indexed folder and then use “Move to External Folder” from the contextual menu.
The second method sounds more complicated but I usually find that it’s actually faster.
BUT – I have a feeling that neither of these options is what you are looking for?