Is your fusee.bin up-to-date as well? If not, try updating it and see if it works.
Otherwise, turn off your Switch and remove your SD card from the Switch and plug it into your PC. Make a backup of your
atmosphere and
bootloader folders just in case something goes wrong and remove them afterwards from your SD card. After that, download the latest fresh Atmosphere and Hekate from their official repositories. While you're at it, you'll need a new hekate_ipl.ini which you can grab from the
sigpatches thread, as well as latest
sys-patch. After that, put the SD card back into your PC, launch RCM mode and send the latest fusee.bin payload and, hopefully, it'll work this time around.
You can check the
NH Switch Guide.
Additionally, you'll need to find firmware files for the Switch on your own because we aren't allowed to link to them here (quick Google search is all it takes to find them). Or you can update your stock firmware and dump it as mentioned in the guide above, it's up to you.
For game backups to work, you'll need latest
sys-patch (for firmware 19.0.0 or newer and Atmosphere 1.8.0 or newer)
If you plan on connecting your emuNAND to the Internet, make sure to setup
90DNS or DNS MITM in order to block Nintendo servers.
For keeping your CFW up-to-date, check
this guide.