If it's "gone back" to the factory tune, I.E starts, drives and "works" so to speak, is it possible OP has accidentially "restored" to default using the data init menu??
The tune itself is kinda burned in ROM so to speak, and will load it's running config based on what's saved to it's memory on the chip, just like a PC would when booting up into Windows.
I don't believe there is a 'backup' battery E.G a cache battery like a PC motherboard either.