I have exactly the same problem. I tried to move away from Refworks, where I cannot export my database including the attached PDFs. So I downloaded the trial version, exported my Refworks database as RIS, and imported it in Endnote. Then I tried to import all my PDFs via “Import File”. Now I have hundreds of duplicates and not enough time to clean them up. I thought that Endnote could help me save time, but without a feature like merging entries, it’ll cost me more time than it saves. So that’s the end of my test.