I'm having a similar issue. I have followed the guide and managed to get into the RedNAND the first time, but now that I updated it, I get a black screen.
O3DS running v9.0.0-20U using menuhax and all the updated files told in the guide
Going to try and restore RedNAND by cloning my SysNAND over to it since SysNAND is still working fine
EDIT: So the clone got RedNAND booting again. Went to the System Settings Emu 9.0.0-20U; all good. System Update > An Error Has Occurred. System reboots. Replaced with Luma Version 5.2 as recommended in one of the comments. It managed to boot up again, but still refuses to update. "An error has occurred. Unable to update. The system will now be restarted."
EDIT2: I'm an idiot, because I have been blocking Updates from Nintendo because I have a WiiU I don't want updated, it wouldn't update my 3DS. Ignore my dumbness