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Okay - just ran into a massive issue. I tried updating Smash Bros. 3DS using the eShop. Got error 007-2999 and upon exiting everything on SD card no longer shows up on the menu. I tried reinjecting my 4.5 nand from Palantine and injecting all the license files from it back into sysnand - it's still gone. Please don't tell me it's an issue with the SD card and I just lost everything......
My nands were linked. But I don't know if downloading something from the Eshop would cause it to fuck up like this.
Just ran a file compare on a CIA I had installed and backed up to my PC vs the one on my SD card. Identical. What is going on?
You need to unlink your emunand. The tickets to games you installed on sysnand or emunand but not the other means that if you visit eShop or Data Management on the one that didn't have the tickets will cause the effected games to be removed.