I have as well.
However, it was more so because I stopped playing for eight months. I know how to go back without losing any villagers...however I was a little careless and absent minded.
Not to mention before my hiatus...I did lose one of my favorites. I also never really liked my map in my original copy...but by the time I learned about all the ways to get what you want...I was too invested with my characters badges, museum, and villagers. This is actually my first day back here in a long time.
So I decided to take my third copy and restart it to convert it into my new main town. I previously only used it for storage, time traveling, and cycling. It took a bit of time to transfer all my things to the others. However, since Monday, I have found a good map and fruit. I also like my mayor's face more. I also started fresh with a new town name.
I'm excited to have the layout I want.
I'll probably keep my original as the storage town until I get my new mayor's catalog complete.
Best of luck to you with your new town!