Please read whole post before following directions.
Disable internet unless the guide says to connect.
To backup SysNAND, Download Decrypt9
https://github.com/d0k3/Decrypt9WIP/releases/tag/20170607
Copy the Decrypt9WIP folder from the Zip file to the 3ds folder on the SD card.
Reinsert the SD card back into the system and boot into EmuNAND, launch Homebrew Launcher and launch Decrypt9.
In Decrypt9 locate the option to backup SysNAND, once done backing up copy that file, along with EmuNAND backup and SD card backup to your PC for safe keeping just encase something really bad happens.
At this point break menuhax by changing the theme. You will need to copy the Nintendo 3DS folder to your PC again. You should have 2 copies, one before you broke MenuHax and one after. Keep track which one is which.
Go to the site
https://3ds.guide/ and follow the guide to the letter. Since you are on 9.2, you will be using the SoundHax method.
Follow the guide through and note Step 6 - Section 2 follow Move EmuNAND.
On this page if you don't have any GBA VC saves skip to section Section IV - Copy EmuNAND to SysNAND.
On step 3 where it refers to nand.bin use the EmuNAND bin file you backed up to your PC using emuNAND Tool.
Skip to Section VIII - Format SD card - since you are already backed up everything.
When restoring the SD card you really just need the Nintendo 3DS folder with the broken Menuhax (2nd backup)
and all the files and folders from Step 6 - Finalizing Setup
Continue where you left off on Step 6
- Section II - Updating the System
If done correctly, you should have all your games/apps, be on firmware 11.6 and have B9S installed with the recommended apps.
If you fell like you are over your head and would like a helping hand I can voice chat you through over discord, (in a few hours)