If it is asking to wipe your n3DS when doing system transfer, doing an emunand backup should do the trick. I did this back when I didn't have any large cia's installed so I can't remember if I found a way to avoid wiping.
But I do remember that I backed up my emunand, did the system transfer, and then restored my backup emunand (it had my custom themes on it and some homebrew).
Since the NNID is tied to the serial number of the console you can just restore a backup of emunand and sign into your NNID again on the new system. Literally all the system transfer tool does is re-register your NNID to the new serial number (this is why when ppl swapped serials to get around system bans, they had to make new nnids).
So go ahead and try these steps:
1. Backup your n3DS emunand (using emuNANDTool)
2. Make sure you backup the entire microSD card to somewhere on your pc.
3. Whilst in latest emunand on both systems do a system transfer, the system transfer tool will wipe your n3DS mSD card and basically clone everything from your o3DS SD card to your n3DS (this is why it gets wiped when transferring).
4. Restore the emunand backup you made earlier.
5. Restore the backup you made of the microSD card back to the card.
6. Boot to emunand and everything should be as it was before.
7. Go to setting and see if you are logged in, if not, sign in again to your nnid and it will work.
This way you won't have to re-install everything. I've done the above steps going from o3DS with rxTools, to n3DS with rxTools and everything worked just fine.
Luma 3DS needs A9LH, which I've heard can fix bricks because it can boot code before the system (like on the wii), so I wouldn't worry about bricks if you're already on A9LH.
When you are done you can reformat the o3DS, restore to a non-hacked sysnand backup or whatever if you want to, and then you're ready to sell.