The "easiest" way would be to backup your current legit NAND, go do your stuff it in airplane mode with Checkpoint, then when done backup the modified raw save from your NAND to your PC, restore legit NAND back, and copy the modified save back (that is in SYSTEM partition /save). It will work.
you need to backup/mount your modified NAND and copy the raw modified save that is in the USER partition (not SYSTEM, sorry my mistake) to your PC. Then after restoring your clean NAND, copy it back (if it needs renaming to match the old save, rename it).
Usuually you can isolate the file by sorting the SAVE folder by date. The file name for the raw save should be something like 0000000000000XX (some numbers or letter).
How extremely inconvenient to go through all of this just because you fear being banned for homebrew.
Has anyone actually been banned for using homebrew only? No backups, no cheating, no illicit nsps. I don't think so.