Shut your ds off, take the sd card back out, and make sure you put it back in right. Sometimes it can be kinda finicky.
If you have a physical copy then you have nothing to worry about really
did you have digital or physical
If you have a physical copy, your SD card has pretty much nothing to do with it.. besides pictures and extra data. If it doesn't recognize your SD card, your town wouldn't be corrupted because it wasn't the cartridge.