Finally after a number of tries I got the device back to live. My procedure:
1. prepare sd-card: wrote the file cm-fx6-firmware to a plain sd-card using the command "sudo dd if=cm-fx6-firmware of=/dev/sdX bs=1K skip=1 seek=1 oflag=dsync"
2. booting from prepared sd-card
3. flashing the firmware to SPI using the procedure described on Compulab's Website (https://mediawiki.compulab.com/w/index.php?title=CM-FX6:_U-Boot:_Firmware_Update)
The selected boot-mode (pin P2-117 = high-level) works as follows: a) sd-card --> if not present b) SPI-flash
If pin P2-117 is pulled to low-level it tries to boot from SPI-flash only.
OTG-USB seem to be unfunctional.
Next I'm trying to install the cubox-i ambian image on my Compulab Utilite Pro. Hope that's working...