You mean it was in Nintendo 3DS\[id0]\[id1]\titles ? It would be useful if you would kindly answer the other questions: was it there before you copied the files off the card, or did it appear afterwards?
https://www.3dbrew.org/wiki/Title_list/Patches notes that a folder named 00030800 would be associated with Mario Kart update data, so at least it's not completely unrelated to what you were doing – but there's no reason there should be files there, nor is there any reason it should suddenly cause everything to disappear.
Anyway, since you took your card out and put it back in again, it's possible there was some kind of loose contact in the slot.