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The config savegame definitely appears to store information on the panel settings. I removed just that save game and allowed my 3DS to make a new one. (it acted like it was reset. After setting it up again, the only thing I actually lost was my primary Mii. But my FC and other data was still there). After that my LCD panels returned to normal.
You can find that save game in CTRNAND FAT16 partition at the following folder location:
Data\[Folder with really long name]\sysdata\00010017\00000000
The "00000000" being the save data file it self.
"[Folder with really long name]" is a folder consisting of a long string of numbers and letters. That's unique to the console and is linked to the movable.sed folder found in the private folder. Note you can't just move the config save game from a different console (or even a different emunand of the same console if that one was seeded from a different movable.sed) since you also need to copy over the movable.sed file. Also note that this folder's name matches the name of the folder the 3DS will generate on in the Nintendo 3DS folder on the SD card.
To safely move the movable.sed file from one console to another, you have to zero out the first 4 bytes after the "SEED" header and delete any data after 0x120 (immediately after the KeyY data). Once you do that , you can use the config save data file that was linked to that movable.sed. You should allow it to create the initial folder in the data folder first by allowing it to boot at least once with the new movable.sed. You will be presented with the language select screen. At this point you don't have to continue. Just power it off and extract emunand partition and inject the relevant files.
Hopefully something will get released that allows extracting/injecting content of data folder as that is still tedious to do right now. Ability to decrypt/encrypt the save data located there would also be great. One could then try and edit the config file directly once it's known where the LCD Panel settings are stored.
You can find that save game in CTRNAND FAT16 partition at the following folder location:
Data\[Folder with really long name]\sysdata\00010017\00000000
The "00000000" being the save data file it self.
"[Folder with really long name]" is a folder consisting of a long string of numbers and letters. That's unique to the console and is linked to the movable.sed folder found in the private folder. Note you can't just move the config save game from a different console (or even a different emunand of the same console if that one was seeded from a different movable.sed) since you also need to copy over the movable.sed file. Also note that this folder's name matches the name of the folder the 3DS will generate on in the Nintendo 3DS folder on the SD card.
To safely move the movable.sed file from one console to another, you have to zero out the first 4 bytes after the "SEED" header and delete any data after 0x120 (immediately after the KeyY data). Once you do that , you can use the config save data file that was linked to that movable.sed. You should allow it to create the initial folder in the data folder first by allowing it to boot at least once with the new movable.sed. You will be presented with the language select screen. At this point you don't have to continue. Just power it off and extract emunand partition and inject the relevant files.
Hopefully something will get released that allows extracting/injecting content of data folder as that is still tedious to do right now. Ability to decrypt/encrypt the save data located there would also be great. One could then try and edit the config file directly once it's known where the LCD Panel settings are stored.