The reason is when linking Sysnand and Emunand will share the same Nintendo folder on your SD while having different ticketblobs. When Emunand installed more games than Sysnand, all of them on Emunand will be archived completely when trying to access Sysnand after a deep reboot, access Data Management or download game on eShop. Because Sysnand's ticketblob doesn't recognize the installed data.
Thus, we need to unlink them. When booting to a wrong nand with wrong Nintendo folder, the system will ask you to DELETE rather than DELETE without asking when linking nands.