When endnote imports PDFs from a folder (a setting in preferences) then it moves those to an new folder (imported). Then if you add new PDFs to the folder, it will import those the next time, and move them. This avoids your needing to do anything. So I suggest you drag the new PDFs to a folder and automate the process. I then routinely delete the imported papers or if you prefer, keep them as well somewhere else in topic locations. Endnote has no way to only import new PDFs if mixed in with PDFs already imported.
