Checkpoint. If you have EU version then it’s the 00001261 folder in extdata. Be careful about overwriting card1, card2 and card3 files directly because you will break the ability to save the game if you do. You will need to delete the files first(Citra side) then just place the ones from your 3DS in there. PS those files are only compatible with your character(s), otherwise bad things happen. They represent character 1, 2 and 3 and it stores equipment sets, guild quests pool etc.
The quests themselves are quest1, quest2, quest3, quest4 and quest5 files those are safe to just overwrite.