Future reference for anyone playing on 3ds. You'll have to inject new versions of the game but if you follow these instructions you should be able to keep your save files:
https://digiex.net/threads/3ds-gba-save-backup-and-restore-with-godmode9.15395/Basically I dumped my save, updated the save on my computer, injected a cia for the new version of Clover, then injected my save file back in.
