Afaik, if you have a Switch with Hekate, it takes over the boot process and decodes package1 and 2, which are the primary and secondary bootloader.
After you end up in Hekate, it decides whether to boot into the official OS/firmware or use a custom firmware.
Although you might have set up a custom firmware and emmc, those 2 bootloaders are shared with the official firmware/OS.
Do you get any other error message or is this the only message you see before ending up with a black screen?
If your bootloaders are broken, you usually will see a message saying that the package cannot be decrypted.
If Hekate is broken, many funky things or just black screens might happen.
In many cases, updating Hekate solves a lot of such issues.
Keep a copy of you SD around because it also contains stuff like your games and Hekate/Atmosphere settings.