It's been a while but iirc whenever I switched from emunand to sysnand my joycons would only work wirelessly on one or the other. I believe this is because it treats the emunand as a different switch as far as the joycon connection is concerned. Like they are paired with one nand, not the other.
So as long you don't have airplane mode on, you have to resync them wirelessly every time you switch between nands. Only way to avoid it is to leave them docked on the switch and it will auto detect them when connected but only while they are connected, not wireless.