No it's not possible!
I hardmodded a 3DS XL made backups of my NAND, installed all legit/clean cia's to sysnand, upgraded sysnand to 9.6, checked if i could redownload them, so i wiped half of the pre-installed games, i could redownload them all.
Then i did system transffer from a 9.6 sysnand to 9.6 sysnand on another 3DS XL, NNID is transffered fine, all free downloaded games showed up fine on the target 3DS XL, but NO legit/clean games
- Doesn't matter if you link NNID or do it without a NNID, it will not work
(Before you say more: Yes i tried different options
- Emunand to Sysnand with NNID
- Emunand to Sysnand without NNID
- Sysnand to Sysnand with NNID
- Sysnand to Sysnand without NNID
- Sysnand 9.2 with all pre-installed games, upgraded to 9.6, system transffered to Emunand with NNID
- Sysnand 9.2 with all pre-installed games, upgraded to 9.6, system transffered to Emunand without NNID
The legit/clean cia's from the pre-installed games never came over to the target system.
You could however redownload all pre-installed games on the source again, even with a different NNID
(System transffer wipes all your NNID information from the source as it now belongs to the target, so you need to setup a new nnid on the source)
The hardest part of this all? the 7 day wait before you can do a new system transffer
I did have more consoles at my hands to test out, but most are back to there owners now.