AC:NH won't boot with any LayeredFS mods

Without the mods, AC:NH is 100% playable.

But with any LayeredFS mods, it won’t boot

How do I fix it?

In order for us to provide better support, we need to see the log generated by Citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File.

Either the mod is not 100% stable, or yuzu requires some changes in its file system emulation to handle it properly. Not something you can fix on your own unless you are ready to get your hands dirty with code.