In general, creating emunand by default the two nands will share the same Nintendo folder.
The problem is if your emunand has more games than sysnand when you download something on sysnand or just deep reboot all different games on emunand (compare to sysnand) will be deleted completely.
Solution: after setting emunand up and testing it without any issue. Boot to sysnand and do factory restore (WITHOUT MEMORY CARD PLUGGED IN) to unlink from emunand. From now on, rename Nintendo folder of emunand to NintendoEMU and sysnand to NintendoSYS. When booting to specific nand, rename the related folder to Nintendo.
Booting to a nand with the wrong Nintendo folder, the OS will ask you to delete > just press power to power off and rename the right one.