When I connect the firefly 3399 with my ubuntu laptop, I get a following error Unable to assess firefly 3399 / Unable to open MTP device '[usb001,039]'.
An update to this thread. I could not fix the problem above but could flash ubuntu on firefly with the windows tools. It worked for me as given in the documentation. Please not that you will be two version on the Android upgrade tool, one to erase the firmware and the second to flash the new firmware.
I'm very surprised that there is no answer for any thread for AIO-3399C ...
In order to flash your device with any image (Android or Ubuntu), you need to enter bootloader mode and use the "Linux_Upgrade_Tool". As You said in your message, you will need 2 versions of the tool.
The wiki does not describe very well the different step, it took time for me also to succeed in flashing Ubuntu from Android 7.1
