Blanc, it should be possible to unlock PDFs with this test script. If it works (i.e. an unlocked PDF is written to the desktop) then setting the output path to the input path should overwrite the locked PDF. Not sure but I think I tested it back then.
If that works it should be possible to unlock PDFs via script in DEVONthink.
(I’m not looking into this again, but maybe someone wants to test it. If overwriting a given path with an unlocked PDF works then there still might be some other problem (e.g. loss of PDF metadata), otherwise I don’t know why I didn’t post a full script)