so, this is what i understood.
you will buy a new console, and you don't want to get a new micro sd card for that new console and want to use another smaller card on the old console
if you DON'T have emunand, the only thing you have to do is move all the files from one sd card to the other
the only files that are required are theese ones:
the Nintendo 3DS folder has the 3ds stuff like your installed games, your saved games, themes, everything related to the oficial firmware. if you make a system transfer that folder will be moved to the new console, if you delete it, the console will boot but you will basically have a almost clean console.
the 3ds folder is not actually needed, it's the homebrew launcher files and stuff
the files named "slot0?????" are the apps that load when you boot the console with certain keys, for example, L+X will launch uncart which is the slot0x25KeyX.bin file
IF YOU HAVE EMUNAND and want to keep it, it's a bit more complicated