That error usually occurs when the hekate/atmosphere version is too old for the official firmware.
Try the latest Hekate and Atmosphere versions.
Don't forget to update the primary payload file called payload.bin as well on the SD card if it exists.
Interesting problem to solve. I accidentally connected a Joy-Con quickly before realizing it hade come in contact with alcohol. I somehow manage to boot into hekate after noticing the Joy-Con was not working. Now I can boot into sysMMC. And I...