If a conflicting setting is made that isn't caught by the GCS setup or flight firmware, it can lock up and refuse to boot. It will retry the boot. If it tries 3 times, it gives up and loads default settings and boots with those. It sounds like that is what happened? You can watch the FC LEDs to see if it looks like it is booting 3 times.
If you know what setting change caused this, when it boots with default settings, you can change just the bad setting back to a good working value, then it will boot normally with <most> of the rest of your settings back the way they were.
You will loose the other settings in that same UAVO/area. That is because any settings change stores the whole UAVO and you saved that UAVO with (at least mostly) default values.
I doubt the following, but here it is: AutoTune does write PIDs permanently when you disarm. I suppose it is possible that you disconnected power in the middle of a config write which could leave the "file system" in a confused state, like pulling the plug on a computer when it is writing the disk.