Hi @guylaine, I’m the author of the “Papers to Bookends” export script that you mentioned using (glad to hear it worked for you!).
To also associate your original reference keywords with the indexed PDFs in DEVONthink, you could try my Papers to DEVONthink script. This, of course, assumes that you still have your original Papers library available.
You could also take the script as an inspiration to develop a script that directly does want you want. E.g., take the reference(s) selected in Bookends, index its PDF in DEVONthink, and set the index entry’s keywords and label accordingly. Similar to Papers & DEVONthink, Bookends is nicely scriptable, so this should be doable.