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Do you have a backup of your emuNAND from before you transferred? That would be the easiest way. Restore that (either to sysNAND or emuNAND, whichever), put the unaltered SD card contents back, boot it up, and back up all your saves using JKSM. You can then restore these on the target also using JKSM (just copy over the JKSM folder that gets created when you backup your saves, run JKSM and import the saves).I didn't reformat the SD card, so technically, the emunand should still be there right? Wasn't able to boot the homebrew launcher so I didn't bother backing up the emunand in the end.
And it's a big ouch on the save files, since I redownloaded both Animal Crossing and Majora's to see if the transfer worked proper.
It's a mess, I backed up the 4GB n3ds card and just took the 64GB one and switched it in the n3ds. But I have all this data from the old games on it and without really knowing how to delete the games from it, or at least nothing major...
What would be the best way to clean the SD card and losing as less as possible?
If you don't, then put the SD card contents on the target console, and run tikShop to reinstall any tickets you are missing (only for games of your region on the titlekeys database - if you installed out of region games, find them on the titlekeys database site, show the QR code for them, scan with FBI under remote install -> QR code, decline to install from cdn or else the save file will be erased).