I am getting a New 3DS XL soon and I am planning on transferring my games/data/Homebrew, and I want to make a backup of my whole system in case I screw something up.
I want to backup everything on my old 3DS, which has Homebrew on it.
Since all of the homebrew data is stored on the SD or micro SD just backup your leftover 3DS software (internal and cartridge software).
Link your Nintendo ID via Nintendo 3DS data transfer in 3DS systemoptions. Then put the SD or micro SD on your pc and make a backup.
Homebrew/jailbreak the new console via https://3ds.hacks.guide/key-information.
Then after finalising the homebrew, transfer the savedata from /3ds/ (stores homebrew data) and from /nintendo 3ds/ (stores normal 3DS data) to your SD or micro SD and reinsert it into your new console.