@matana when you make an emunand, it takes a copy of your entire switch and puts it in a different location (your micro sd card). what you do on your sysnand won't affect anything on your emunand and vice versa.

emunand does have options for installing on system memory and SD card but yeah, it's all localized to the emunand and won't touch your sysnand at all no matter where you decide to put stuff unless you manually go through the files and do it yourself, which i don't think is possible for games or saves. games would obviously get your sysnand banned, but most saves with a homebrew app are totally fine swapping back and forth. some games might check though so i'd look it up first just to be safe.