Re: I would not store critical configuration data in a config file.
i think irrespective of the method of storing the values, testing should have determined they were indeed missing
I've done, albeit as a hobby, work with car ECU's, and although you can start a car with a variety of settings missing or misconfigured, you certainly can't take it past the failsafe region without seeing obvious issues. IE miscalibrate/configure the airflow sensor and you'll be able to start the engine and it'll idle, take the revs above 3,000 rpm (or whatever your limp home values are) and you'll see it enter limp home mode as soon as the other sensors data diverges from airflow.
I'm sure they had a more complex fault than that, simply as they had enough power to get into the air.
would very much like to see more info on what happened, as I can only speculate that it was something like a cloning of the settings from the running engine to the others that put a sensor just out of bounds as altitude increased, but what sensor would read like that is a curiosity to me.