Are you adding your new references to the “synced” library or to a different Endnote library? New references should be added to the library designated to sync with your Endnote online account. You can verify the path and name of the library by going to the Endnote toolbar and selecting Edit >Preferences, then in the dialog box, click “Sync”. The path/library is displayed in the “Sync this Endnote library” box.