This page is a guide on how to salvage save data from SD cards that didn't go through Finalizing Setup and have no homebrew applications installed, or to those that have found their SD card to be corrupted. Two common signs of corruption are HOME Menu applications disappearing after the SD card was interacted with, and issues with applications, such as broken banners or icons in the HOME Menu, Luma ErrDisps stating the SD card was removed, as well as unknown applications displaying in Data Management.
What You Need
The v3.10.0 release of Checkpoint (the .3dsx file)
Copy the /3ds/Checkpoint folder of your SD card to a safe place in your computer
If your SD card was showing corruption signs, it is extremely advised to format your SD card, test it for errors and restore Luma on an empty SD card before proceeding to restore your save data. Do NOT reuse a card that was showing corruption signs if it failed the integrity checks.
Do NOT restore your corrupted Nintendo 3DS folder to the new setup, or errors and further corruption are likely to keep happening.
Section II - Restoring
If you're restoring your save data from a corrupted setup to an empty SD card, or if you do not have Checkpoint already installed, continue to Finalizing Setup before following the instructions below.
Power off your console
Insert your SD card into your computer
Copy the /3ds/Checkpoint folder from your computer to your SD card
Reinsert your SD card into your console
Power on your console
Open each game individually and create a dummy save file in them
Close any running applications and return to HOME Menu
Launch Checkpoint from your HOME Menu
Hold B to refresh games list
Press A on the game you want to restore save data for
Select the backup created on Section I
Press Right Shoulder to restore
Repeat steps 10-12 for all game saves
Press X to switch to extdata
Hold B to refresh games list
Press A on the game you want to restore extdata for
