If you've used homebrew with your NAND, it's probably dirty. If you've installed NSP files, it's very dirty. If you've never used homebrew with your NAND, it's clean.
The sysNAND is the combination of system files on the Switch's eMMC. The emuNAND is a combination of system files emulated on the SD card pretending to be on the eMMC. What you do to one does not affect the other, so it's possible to do use hacks with one and stay clean on the other.
The stock option runs no hacks (no Atmosphere) and keeps the NAND clean (if it's already clean). The CFW option runs Atmosphere and is for homebrew and piracy, and it will make the NAND dirty if it isn't already. See above for the difference between "sysNAND" and "emuNAND."
That means your sysNAND is dirty and should not be used with the internet (unless you have 90DNS and/or Incognito installed). Otherwise, you could get banned.
If you haven't setup an emuNAND, then you cannot boot into emuNAND.
As I explained above, stock means Atmosphere/CFW is not run, so your NAND is kept clean (if it's already clean).
Using an emuNAND is like having an entire clone of your Switch system on your SD card. If you use emuNAND instead of sysNAND, then it's going to bypass the actual Switch system and use the copy on your SD card instead. That means you can do anything to one without affecting the other.
- When I say emuNAND, I mean emuNAND. When I say sysNAND, I mean sysNAND.
- You can use CFW (Atmosphere) with either sysNAND or emuNAND.
- You can use stock (no Atmosphere) with either sysNAND or emuNAND.
If you have used CFW/Atmosphere on your sysNAND, it's dirty. I don't even know if you have an emuNAND. If you want to use online play, it is recommended that you do the following:
- Create an emuNAND on your SD card if you haven't already. Follow one of the guides. It will require re-partitioning your SD card on your computer.
- Restore the clean NAND backup to your sysNAND.
- Update the sysNAND to 8.1.0 if it isn't already on 8.1.0.
- Update the emuNAND to 8.1.0 if it isn't already on 8.1.0.
- Use the sysNAND for online play, and use the offline emuNAND for hacks.
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If you cannot see your SD card with your Switch after setting up your emuNAND using one of the tutorials out there (there's a link to one above my posts), then you did something wrong, and you will probably have to re-partition your SD card properly.