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.
Sounds like its like some sort of serial number or something attached to the save and some internal storage or something, so if you try to copy / move your save game it'll look at the save and assume its corrupted or not yours and basically ignore it, starting again.
decent step to stop people from just effectively giving their village out to others.
Does that mean if someone inserted a physical copy of ACNL to their 3DS after already downloading a digital copy it would make 2 towns? :/