No no, I only have one copy of each file. I simply use DT as a file browser/organizer—which is where its real strengths are anyway. I can read my PDFs in DT, but if I want to annotate them, I can double click the file name to open in an external editor (you can identify an external editor in settings). Then annotate, close, and voila. If I don’t modify it in DT it remains searchable, at least so far.