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

Heran Bago

Where do puyo come from?
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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.
 

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