Depending on how the registry is configured (ref topic 2453), you might be able to override the app in the flash disk by inserting a CF card with an EXE file in the Startup folder.
Otherwise, set the DIP switches to get to the bootloader menu on the debug serial port and erase the portion of flash memory where your flash disk resides.
We can give you more explicit pointers, if needed. Drop us a line at support.us@eurotech.com.