There are many reasons for this message :
- You're injecting an old version of Hekate/Atmospere's primary payload. (If you have an unpatched Switch, you need to get the payload that matches the files on the SD card. USB injectors like the RCMLoader need to be update sometimes).
- You got some old configuration settings that you're trying to use with a newer version of Hekate
- Hekate can't find the emummc partition because the config file points somewhere else.
- Files on the SD card are somehow corrupted
- The bootloader partition has somehow been corrupted.
The first 2 are the most common issues.