Whichever NAND gets formatted will be reset as new, so any games and saves on it will be lost. If your sysNAND has games installed on it and you cloned it over to emuNAND, then formatting sysNAND will make it so you can't access those games from sysNAND, but they will still be there in emuNAND.
Before formatting anything, it's strongly recommended that you use emuNAND9 to dump sysNAND to NAND.bin and emuNAND to emuNAND.bin, then save the two files to someplace safe on your PC. Then take a complete backup of the contents of your SD card.