If you go to the Help menu in the Indigo client, you'll see an item that says "Managing a Z-Wave Network". Click on that, and it will take you to the Indigo Wiki page for Z-Wave networks. In essence,
If a Z-Wave device is no longer available to your network (it failed, etc) then you can use this menu item to remove it from the interface. You might need to attempt a Define and Sync on the device (and allow it to fail) - just create a new device, try to sync it, when it fails then try to remove it.
If you no longer have an Indigo device linked to the broken Z-Wave device, you can attempt to create one and link it to the failed device (as the quote above notes). After that, you should be able to remove it using the instructions.