I tried reformatting the micro SD Card and I ended up with the same error. It might just be the program or that the emuNAND.bin wasn't extracted correctly?
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oops, sorry for double post
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I managed to fix it using EmuNAND9 via HBL.
I followed this tutorial if anyone is curious:
"
2: Boot into EmuNand 9 from Homebrew launcher on the OLD SD CARD
3: Once booted into EmuNand9 go to EmuNand Manager Options>Dump EmuNand to EmuNand.bin
4: Once it is completed go back to the main menu of EmuNand9 and press "Select" to Unmount the OLD SD CARD
5: Transfer EVERYTHING from the OLD SD CARD to a back up folder on your PC
6: Install the EmuNand9 folder to the root of the NEW SD CARD
7: Plug in the NEW SD CARD into the 3DS and press "B" to remount the NEW SD CARD
NEW SD CARD will be erased to be sure to back up your data
8: FORMAT the NEW SD CARD by going into SD Format Options>Format SD & setup starter...
This will allow us to not have to go back to our PC and reinstall EmuNand9 to create the EmuNand Partition
9: Once Finished, Go back to the main menu of EmuNand9 and select "Complete EmuNand Setup"
10: When that is finished Press "Select" again to unmount theNEW SD CARD
11: On your PC, Move over ALL the OLD SD CARD Data to theNEW SD CARD
THE REST OF THIS GUIDE WILL BE ON THE NEW SD CARDONLY
12: When the Data is finished transferring to the NEW SD CARD, Eject the NEW SD CARD
13: Remount the NEW SD CARD to your 3DS
14: Inside EmuNand9, choose EmuNand Manager Options>Clone EmuNand.bin to EmuNand and wait for it to finish"
