Cjua,
When you talk about a VI on the cFP-2020 it sounds like you are just targeting the RT Engine on the cFP-2020. This means that you are loading the VI onto the RAM of the module and it VI runs from there. The VI will continue to run as long it is in RAM, of course as soon as you shut down the cFP-2020 the RAM loses power and there for its memory. So the VI that was targeted there is lost. So power cycling the unit will automatically erase a VI that was targeted to the unit.
Now, if you are talking about an executable that you have built from a VI, and then downloaded to the cFP-2020s flash memory. This would be persistant from power on to power on. This is of course how you deploy applications to FieldPoint for long term use. This executable would get loaded into memory (from flash) everytime the unit starts. If that is causing the glitch you are seeing and you need to delete that, they easiest way to do it is to FTP into the cFP and erase the .exe. So in any web browser FTP into the IP address of that unit, and you can then navigate to your .exe and delete it from the unit.
I hope that does the trick for you, and comes to you before your demo. Good luck.
-GDE