Heya, just created an account here, hoping to be of help.
I've installed CFW on 2 of my 3DS i have here at home, and i got that exact same problem on my Japanese 3DS XL when i installed CFW (couldn't install the latest version through the system menu)
I managed to fix it by installing my 9.2 NAND that i created a backup of a couple steps earlier through hourglass9, and choosing keep a9lh, and after that i managed to update without any problems.
If you've been using the plailect guide, you should be in version 2.1.0, be done with the a9lh installation and have a backup of 9.2 too.
I'll just say that i'm kinda new to all of this, so when that happened to me i pretty much decided to experiment a bit, and yeah, it solved the problem for me xD
So, if you're unsure, you can always wait for someone with a bit more experience about CFW and stuff to jump in here to help.
Hope everything works out fine, and you get it fixed. Good luck!
Edit: If you decide to try the 9.2 backup way + keep a9lh. Remember to doublecheck your Luma3DS settings before you go on updating (section 3, part 1). Extremely important.
- “Autoboot SysNAND”
- “Use SysNAND FIRM if booting with R (A9LH)”
- “Show NAND or user string in System Settings”
- “Show GBA boot screen in patched AGB_FIRM"