Good question. Maybe just mark each Nintendo folder for each respective console?
Are you trying to launch them in OFW? If not, which CFW did you install them under?
Apparently, LayeredFS is enabled by default in the "CFW" Launch Configuration. Wish they made that a little more discreet.
If you want to be safe, you will have to be constantly making new NAND backups every time you intend to go from legitimate online to play to offline hacking. In order to preserve your hacks, you can either back up the individual parts such as saves with a save manager or perform another NAND backup just for the hacks. If you are going with the latter scenario, making a backup with the ReiNX toolkit is more favorable than Hekate since the NAND will be tainted anyways plus the ReiNX toolkit dumps the NAND much faster than Hekate.
You can update your firmware without burning fuses using the homebrew application ChoiDujourNX although it installs AutoRCM as a precautionary measure to avoid fuses from being burnt. However AutoRCM can be a boon in the right hands if managed properly.
ok i didnt explain that, the data the switch creates on the sd card for its games so in this example im looking for the folder which houses the all the extra data for xenoblade 2 so i can move it onto a different sd card. the path for the folder im mention is ( \nintendo\contents\registered\).