From your description I get the feeling that there is something wrong with how or where the system has mounted the external disk.
Please note that it is not recommended to mount storage devices to folders that are not empty, so make sure of that (detach drive, check if folder is empty and if not empty it, then reattach drive) If this does not solve your problem, try the following procedure:
Please run "mount -l" (that's lowercase L) on a terminal. This will print a list of all mounted partitions. Look for your external disk name.
If you are not sure about the name do the following:
- Shut down the computer (to unmount all filesystems)
- Disconnect the external drive and reboot your computer
- When boot sequence completes, open a terminal
- Now reconnect your external drive, wait a couple of seconds and type "dmesg" on the terminal. This will produce a long list of messages but you are interested in the last 10 or so. Look for something like :
[some_numbers_here] sd more_numbers [sdx] Some_message
The x in sdx can be a, b, c, etc depending on the number of drives you have installed in your system. If you have only 1 (sda), then the external drive will be sdb. If you have two internal drives (sda, sdb) then the external drive will be sdc and so on.
A note here: These are physical drives and NOT partitions. Partitions are designated by a number being appended to the physical drive name,like sda1, sda2, etc
Now that you know the drive name type "mount -l" on your terminal and look for the line that describes where your external disk is mounted. If you have not mounted any other storage device after connecting your external drive it will be the last line displayed. eg.
/dev/sdb1 on /media/folder_name type fuseblk (rw,nosuid,nodev, ...
This folder_name should be the destination of your copy command.