Well, I guess I can't convince you that factory reset, start from scratch, start fresh... isn't a good idea. Same for the fact that there doesn't seem to be any ban risk on 3DS. I've done my part.
Since ntrboot can be performed completely offline, you can just follow the guide normally, install CFW, backup saves with Checkpoint/JKSM and use Format System Memory after that (I still wouldn't do that as it creates more work for nothing)
Or for the purist "I do not want to write to NAND" two possibilities:
A) ntrboot into Luma3DS
- Have Luma3DS boot.firm and Homebrew Launcher boot.3dsx in the root of the SD as well as the .3dsx versions of JKSM/Checkpoint in SD:/3DS
- Perform ntrboot, the OS will load with Luma3DS CFW if done correctly (nothing is modded though)
- Rosalina injection for starting HB Launcher in "Download Play"
- Use one or both of the save managers to backup the saves
B) ntrboot into GodMode9 (I'll not type that all out -- far too much work)
- Have GodMode9.firm renamed to boot.firm in the root of your SD
- Copy movable.sed to SD card
- SD:/Nintendo 3DS/<ID 0>/<ID 1> can now be decrypted with ninfs and 3ds-save-tool can extract the saves