You can clear the VI on the node by holding down its reset button ~10 seconds. This will cause the node to factory reset with no VI on the node. You will know if it worked if the node's signal strength LEDs begin flashing Outside LEDs<---->Inside LEDS.
The Undeploy option in the LabVIEW project undeploys I/OVs that may not be used anymore. It does not undeploy the VI as you have discovered.
Cheers,
Brian A
R & D Product Support Engineer | WSN/Network DAQ/Wireless
National Instruments