Homebrew Backup SD card, format 3DS, restore backup. Saves ok?

[Heran Bago]

If I copy the contents of the SD to a computer, format the 3DS with the system settings menu, and then copy everything back, are the save files and games downloaded from the eShop still usable?
I seem to recall that this stuff is tied to the system and belongs to a different 'system' when you format, hence why wrapped gifts don't show up in the other when you format sysnand or emunand.