How are you updating it?
The bot has an installer and i've never had to make a new folder unless it was a switch from beta to release and that's just cuz it makes things easier rather then updating every plugin that isn't updated yet.
I always download the latest beta manually and set up everything. It worked for me all the time.
I've tried to update it automatically, but there is always some "error" and updating process fails to complete for some reason, so manual updating is the only solution. I haven't even tried the auto update in a while, maybe they have improved it.