So, I found how to use Checkpoint, you need to hold 'b' to refresh your SD game list and then you can just restore your backed data to the new app
this post was submitted on 27 Dec 2023
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3DS Hacks and Homebrew
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There is an official app to do just that! If you have the hShop, it'll be under DSi tools. It's just called "Save Data Transfer Tool."
I don't have internet access on my 3ds at the moment, so I cant get specific, but if I'm not giving good instructions, let me know.
If you don't have hShop, it's definitely worth installing.
If for some reason you cant use hShop, I can send the .cia for SDTT to you, if you'd like. =)
I was worried it would brick my device because it needs internet to work (x_x)
Oh... I haven't used it in a while. Sorry about that!