You need to explain what you are trying to achieve so we can better understand and assist?
What EmuNand are you using? Emunand as Hidden Partition or Emunand as files on microSD?
Emunand as Hidden Partition: Format On PC
If you format your SD CARD, it will only format the DATA partition, not the hidden partition.
Emunand as Hidden Partition: Format On Switch
On the Switch => Options => System => Formatting Options => Format microSD Card, if you use this option, this will format the ENTIRE SD CARD, the hidden partition will also be deleted.
Emunand as files on microSD: Format On PC
This will format the ENTIRE SD CARD.
Emunand as files on microSD: Format On Switch
Same as Emunand as Hidden Partition: On Switch above.
SD CARD\Nintendo <= This folder contains your profile, saves, eShop games, updates, etc... on your SysNand.
SD CARD\Emutendo <= This folder contains your profile, saves, NSP installs, updates, etc... on your EmuNand.
So if you have important stuff on your SysNand, this is the folder where all the info is kept: SD CARD\Nintendo
Someone needs to confirm, but I'm not sure if you can copy/move the Nintendo folder to another SD CARD or not? same goes for Emutendo folder.