Fantasy Life is one of the games that are ext data in SaveDataFiler. If you refer to a Fantasy Life save editing thread, they tell you which save to backup. That's because unique games like Fantasy Life, have save data in ext data. Games like Theatrhythm Final Fantasy.
I never tried backing up cia save games, I'm primarily a .3ds user.
I wonder if we can share saves from cia, if we backed them up from SaveDataFiler. I know it's possible for games like Pokemon X/Y/OR/AS, and Animal Crossing New Leaf (Card2 games) But then those were .3ds saves. I don't know if card2 applies to cia games.