Look.
It's as simple as telling the people who do the update debugging and rebuilding that you don't mess with the .dat files, you don't go perusing files related to the important aspects of users' preferences, and you most definitely don't allow the computer to just change the settings at any point.
We're stuck in the decision to use Microsoft because of the few evils, you're not requiring code knowledge in user interfaces (Linux) and you're not bottle necking speeds and trying to create a device that supposedly sits at water damage levels that can be submerged in the Marianas' Trench but can't take a physical fall (Erple).
This is common sense. We shouldn't have to constantly change stuff back and forth. If you gave a log of the updates you put in, a LOT of people would be qualmed. If you focused on what you changed, and kept us in the dark we would probably be just as quieted.
Except; no.
Apple treats their customers like sheep. Don't, please.