I hope I'm not too late to answer, but:
Start the game as a new character. When you're handed the map, see if someone is missing. Or, just walk around and look for all your villagers. If everyone is there, just hit the Home button and get out of there. You can then start the game as your mayor and everything will be fine, but be aware that after all that time, someone will certainly be thinking about moving. So, wait until you get pinged and stop them.
If someone is missing, set your 3DS clock to Thanksgiving two years ago and DO THE SAME THING WITH A NEW CHARACTER. Walk around and see if everyone is there, and make sure to go in houses to make sure no one is in boxes. Really, you only have to worry about the one that was missing when you checked in current time. If no one is missing and no one is in boxes, enter as your mayor and stop the one that moved from moving. Now, you can save and reset to real time. When you start, you will again have a new animal thinking about moving, so just stop them and you'll be fine.
Sorry if this sounds complicated, but it boils down to "use a new character to see if anyone is gone, and if they are, go back to around the time you last played and stop them from moving."
Now, if you don't have the option of creating a new character (you have a mayor and three side characters), you'll just have to set the clock to when you think you last played and hope for the best. If you haven't even loaded New Leaf, you can check your activity log on your Home menu for the last date.
I hope this helps.
- - - Post Merge - - -
If you do that and it works, please report back to us!