EimaMei

That fixed the problem! Thank you so much for helping me with this.

Well I used a homebrew app called FTP-GMX that allows me to transfer any files from my SD card to my pc by connecting to an IP. I used FileZilla to connect with the FTP server. Then I copied /3ds/Checkpoint/Saves/0x01B50 Pokémon Ultra Sun/ to my desktop.

I am not sure since the save has the required size (well it shows for me it's correct, maybe it isn't)

The savefile has the game almost 100 percented. Beaten the elite four, caught available legendaries, completed most of the Pokédex etc.

So I have a copy of Ultra Sun on my homebrewed 3DS. I used the latest version of Checkpoint to get my Ultra Sun savefile to be used with pkhex. But the outputted save didn't work with pkhex and would just give the same error. I have no clue on why it doesn't work. If it adds anything, the savefile is from my real Ultra Sun cartridge. main