To delete a connection file from within EndNote:
From the Edit menu, select Connection Files > Open Connection Manager.
Select the connection file to be deleted.
Select Clear from the Edit menu, or Control+clickright-click on the connection file and select Delete from the shortcut menu.
You can also delete an unwanted connection file by switching back to the Windows Explorer, or by opening "My Computer,"Macintosh Finder and opening the Connections folder in the EndNote folder. Then, drag the connection file from the Connections folder to the Trashselect the file to delete, and then select Delete from the File menu or drag the file to the Recycle Bin .
Note: You must have read/write access to the Connections folder in order to delete a connection file. If you do not have administrator access, you likely will not be able to delete a file located within the Program Files folder.