In EndNote, you can automatically "sync" your desktop and web libraries so that all the references, attachments, and groups in one can be accessed from the other.
Use the sync icon and follow instructions.
To transfer references from EndNote Web to your desktop EndNote or vice-versa, you need to use your desktop EndNote.
6. You can either transfer from Web to Desktop (and specify allow duplicates or not) or from Desktop to Web (showing references, all references in library, or all references in a group). Click "Transfer"
NOTE: You may transfer up to 5000 Kilobytes of data at once.