If you want to update an eShop Nexomon game, use the console’s System Settings → System → System Update or open the game icon while connected to the internet to trigger the official eShop update.
Technically, if your Switch is not banned and you are in a "clean" sysNAND, an eShop update could work for a legally purchased game. However, for an NSP file installed on a modded console: nexomon switch nsp update eshop work
If you want Nexomon updates that work seamlessly with the eShop, stick to the official patch system. NSP updates are for offline, custom-firmware environments only and will never integrate with your legitimate eShop license. For a hassle-free monster-catching experience, buy the game and let your Switch update automatically—it just works. If you want to update an eShop Nexomon