fun fact: if you delete the data folder on your 3DS NAND using godmode9, it will effectively overclock your system, allowing o3DS users to play n3DS exclusives and n3DS users to get a smooth 60 fps in N64 and PS1 emulators!!
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I tried deleteng my NAND backup from my SD card a while ago, and the shutdown speed is like 1 second instead of 5 or 10.
you can also delete system32 on windows to free up space