For CARD1 games, be sure to exit the game properly (Home > Exit) before backin up your saves.
Gateway has a savegame chipset on the flashcart which is used when playing.
The content of that chipset is extracted and saved to the <GameID>.sav when you exit the game.
When you launch a game, the corresponding save file is restored into the chipset, except if you launch the same game than you previously played.
If you let your battery dies out while playing, the save is not backup to your SD card and you will not backup the most recent progress.
If after you let your battery dies out you launch the same game, it will use the chipset content and you can continue your progress.
If after you let your battery dies out you launch a different game, it will replace your last progress with the other game's save file and you will lose your un-backup progress.
To know to which game corresponds the <GameID>.sav files on your SD card, you can make a search of your filename's ID on
http://3ds.essh.co website.
CARD2 games are writing saves in realtime inside the ROM. so you don't have to care about the proper way to exit the game.