Nevermind i got it fixed with someone else's help, but thanks for tryingSomething really weird has happened to your SD card :-/ Does it still boot into your emuNAND when you start it up? What did it say in System Settings for your firmware?
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As long as you never format your system, your Nintendo 3DS folder will continue to work on your console. Backup the whole folder not just the save files or else you might forget where to put them.