I updated my system and than forgot one of my towns was frozen on a date. To fix this I removed the update in the systems and than opened the game. Asked Isabelle to change the date and than did a save/quit. I than went back in the 3DS systems and added the update again. Opened the town and got all players updated. The town is now frozen again.
I did this during the first update and it was a digital copy. I removed the cartridge ACNL that was already updated from the system. Made sure the update was done before I put the cartridge back in the system.