All CF hardware runs a bootloader which is responsible for validating and starting the firmware running.
The hardware can be forced into bootloader mode to ignore the current firmware and await new firmware to be loaded.
This will force the device to begin deleting it's current firmware, as signified by the red 'ERROR' LED flashing rapidly (LED may look on, but its just flashing really fast). The device will then reboot into bootloader mode, and the power LED should remain flashing.
The device is now ready to accept new firmware. It will show up in System Commander with a red indicator in the CFLink Devices list. You can click on it and the firmware tab will become visible to upload firmware.
For more info and options, follow the firmware guides to achieve this.