EmuNANDS are a copy of the sysNAND. They are tethered to that system just like the sysNAND. If you do a System Transfer and want to restore your games, this is how I did it.
1: Made a NAND back up of my source system
2: Did the System Transfer as normal
3: Restored NAND of source system to the source system
4: Dumped the Tickets from source System using Decrypt9
5: Using FBI, I restored the Tickets from the source system to the new system
6: 90% of the games were properly restored.
7: I deleted a few games that didn't install properly, then redownloaded them.
8: Majority of the saves were moved, so I had to backup/restored the saves from the old to the new.
This is detailed in the Guide
https://3ds.guide/2.1.0-ctrtransfer
And Section VII - Reinstalling Tickets
https://3ds.guide/installing-arm9loaderhax