I went and bought some SD cards to save my Animal Crossing: New Leaf data that I wanted to keep for playing casually, so I can attempt some speedruns later. Should I have just waited until another copy of New Leaf showed up?

3DS games save to System Memory / SD card, depending on if you have a SD card inserted - another copy of new leaf wouldn't help. so you need to check that your save isn't on System Memory, otherwise you can switch out carts & SDs all day long to no avail.

If you don't want to spend money on buying x SD cards for your saves, you could also look into homebrew and back up your saves that way.

the only savegames I have on my system are from downloaded eshop games.

Looks like I might need to erase my System Memory. That or see if I can copy it onto one of the cards; I don't really want to lose Fortree, but then again I could always make another. Thanks though guys. =)

Just had a brainwave, could I just buy New Leaf again through the Shopping Channel onto one of the SD cards? Not sure if I need to erase my System Memory or not for it to work.