The teams use a single homologated ECU to prevent driver aids. I would assume it doesn’t have a downlink on-track to prevent tampering, but presumably with umbilical cord connected in the garage during red flag they can make changes, which the FIA probably sent over. Who knows.
The problem happened during the formation lap. They red-flagged the race and brought all the cars off the track. I don't know any more about the update mechanism than you do, but GP's theory is plausible.
