Hacking Doubt about 3DS game saves after system transfer (used for DSiWare Game Injection)

[Shokubutsu]

Hello, everyone. I've just used my Nintendo 3DS (Old) to hack my friend's Nintendo 3DS (Old) usign DSiWare Game Injection Now my SD Card is in my friend's 3DS, and I'm waiting 7 days to make the system transfer back. I made a backup of my SD Card before doing the whole process, but I didn't make a backup of my saves (because there there weren't many important saves).
When I transfer the system back, will I still have the saves? In negative case, is there a way to recover them using the SD Card backup I made?

Thanks in advance.