Let's try one more time:
- check the docs at wiki.ultimaker How_to_upload_new_firmware_to_the_motherboard
- get the latest Ultimaker version of replicatorg version 3 from software.ultimaker.com
And it still fails...
When it fails it tells you to look at the console, so better do that: it complains about not being able to access my usb port /dev/ttyACM0, as there is a problem with the lock file. Ok, that's easy: delete the lock file (maybe it's left behind for some reason...).
Nope, doesn't like that either, but there is progress! Instead of complaining about the lock file it's now getting timeouts.
Time for another look in the console, it shows the command it's trying to run. Hmm, let's kill replicatorg and run the command: avrdude -Cavrdude.conf -cstk500v2 -P/dev/ttyACM0 -b115200 -D ... (all paths are stripped from this example, i just copied and pasted the command from the console without any editing).
And that works!