Delete the Nintendo 3DS folder and place your backup on it. Everything should still be there. If you didn't unlink, I have no idea why your games aren't on Sysnand still.
I managed to fix it. Now I'm going to unlink my nands. I still want to keep the things I have bought on the eshop on my sysnand. Is that possible? It says I have to restore the nand.bin. Will my nands be still unlinked?
It's not possible. So you can choose to either not unlink your nands, or you can simply run TinyFormat in EmuNAND instead of SysNAND. But then you will have to install a cia installer in EmuNAND and you will have to swap between SysNAND and EmuNAND to play all the games.
Ah ok thanks. To make sure I've done things right I have a data, firm,lang, nand, sys and a theme folder in the rxtools folder on the root of the sd card. When I used the cdm firm.py file I got no firmware.bin file but 3 files with many numbers. Was this right?
In SD/rxTools/theme/
create a folder called "1"
Place all the files from Nasty's theme into that folder. It should look the same as the "0" folder.
Then launch the rxTools Menu, go to SETTINGS, and change theme.
Yeah. However, in the advanced options it says error opening /rxtools/theme/2/adv4.b
Maybe nastys didnt create a button for all the options.
However I dont know how to use anything else than rxmode or creating a nand backup so it doesnt matter much
Maybe it's an error reading the Devmode button; it was changed to Pasta Mode recently. It's alright though, you can always change the theme back if you ever need to access it.