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If you’re playing on a cartridge, use Checkpoint to back up the save. If you’re playing via TWiLightMenu++, the save will already be on your SD card. Then just copy the save to your PC, with either an SD reader, microSD management, or ftpd. Then do whatever save editing you want to do and transfer the file back. For TWiLightMenu++, just put the save in the original location, and for a physical cartridge, you can restore the save with Checkpoint.
Checkpoint should already be installed if the 3DS was set up according to 3ds.hacks.guide. The icon looks like a flag. Do you have it?