So, if I was doing this I would take care of sorting the documents into keeper and losers in DEVONthink. And probably move the keepers into other more groups with more granular focus.
Since you are using DEVONagent in conjunction with DEVONthink you might consider a different approach. After the DEVONagent search completes, select everything in the results window and use Data > Summary to export to a single group in DEVONthink a set of RTF notes that summarizes each item found by DEVONagent (usually in around 200 words) plus a link to the original document on the web.
Then, in Tinderbox, watch the group in DEVONthink where you stored the summaries. First thing, is you get DEVONagent to make the summaries for you as a starting point. Second, you get a nice concise file to work with for your note taking, and third you have a link that will take you to the document if you want it. (Also, on High Sierra with a MacBook or MacBook Pro you can force press the web link and see a preview of the source document – internet connection required.)
If you decide you want to retrieve a particular document, select the summary file for that document in DEVONthink and use DEVONthink’s Script > Download > Convert URLs to PDF Documents. If you do this in the watched group, then Tinderbox will eventually get copy of the downloaded document.
Just a few suggestions that might make the process more pleasant.