Maybe Nintendo didn't want people "copying" or making "second" towns on Animal Crossing. So when you started up the game on the other SD card, the game told you that you had another save saved somewhere else, and asked if you wanted to forget about the save and make a new one on the current SD card.
The game will probably recognize saves though some kind of "ID" system. That way people cant share saves. Also, hitting the option gave you a new "ID" so the old save isn't recognized anymore.
I hope I made sense. I'm a Computer Science guy and sometimes I might use to much jargon or go into confusing detail.