well normally, if users try to import a folder which contains more than a main (like having a .bak inside), OR the save file isn't named main,
the game will display the corrupted message.
I'm not sure if all 3DS games have their saves named main, but it seems to be the case.
So the criteria to not having a 'corrupt save' is:
1. The save file must have the same name as when it was exported (in Gen 6-7 case, main)
2. Nothing else must be in the save folder, besides what was originally there