If you have an EndNote Web premium account associated with EndNote version X5 or later of the desktop software, you can transfer or Synchronize (with EndNote X6) your file attachments:
http://www.myendnoteweb.com/help/en_us/ENW/hsr_attachfiles.htm
Jason Berman
Technical Sup Rep RS
Thomson Reuters
Phone: +1 800-336-4474
thomsonreuters.com