To prevent the Fantom-G from loading the internal project during bootup, just press and hold the "EXIT" button. Instead of the saved internal project, a blank project will be loaded.
Το completely delete the internal project (ALL DATA WILL BE DELETED) you can do the following:
Menu->Project->Create->Internal->OK
With this procedure, a default project will be saved in the internal memory, so the Fantom-G can bootup more quickly. Once it boots, you can load the USB-based project of your choice.