The only way for this to happen now is a double event when you log off (erasing the local list), login and immediately follow someone or change relays before the contact list is downloaded.
Discussion
The latest version fixed it? I've never logged out before and have had this happen a few times.
Ah today I did login and immediately follow someone. Then they became the only person on my follow list.
I wish I had a way to protect against this...
Perhaps add a delay where they aren't allowed to follow or change relays until after Amethyst had tried to download your follower list from your currently configured relays?
I forget which client did this, but when the user's following count is zero (rightly or wrongly), a warning could pop-up if the user is trying to publish a Kind 3 event asking them if this really is their first follow.
It's not the most elegant solution but it could prevent people from overwriting their contacts.