I tried to transfer my emuNAND to a new SD card using this guide:
https://gbatemp.net/threads/how-to-transfer-emunand-to-another-sd-card-working-on-new3ds.383684/ but my 3DS doesn't recognize it and my PC says it has to be formatted before use. What do?
They really should remove that guide... I don't think I've seen anyone be successful with it.
Anyways, I am going to assume it's a GW EmuNAND. You'll have to use EmuNAND9 for these steps.
1. On your old SD Card with your GW EmuNAND, load up EmuNAND9.
2. Go to EmuNAND Manager Options -> Backup EmuNAND to file (This is going to backup GW EmuNAND onto your old SD Card)
3. Press the select button to safely eject your old SD Card. Now insert your new SD Card, and press the B button to go back to the menu.
4. Go back to the main menu, if you're still in the EmuNAND Manager Options menu, by pressing the B button.
5. Go to SD Format (EmuNAND Legacy) - This should make a GW sized EmuNAND.
6. Press the select button to safely eject the new SD Card.
7. Now go to your computer, and transfer all the files from the Old SD Card to the New SD Card, including the backed up emuNAND file that was created earlier.
8. Now insert back the new SD Card with all the files, and press the B button to go back to the menu.
9. Go to EmuNAND Manager Options -> Restore file EmuNAND. (This will restore the GW EmuNAND backup onto the new SD Card)
10. You are now done.
Edit: If it's a redNAND and not a GW EmuNAND, then at step 2, do Backup RedNAND. for step 5, do SD Format (EmuNAND default)