Never extract on the same folder! Enter the v0.1.0 folder, enter "game" folder inside it, and put the "saves" folder in somewhere safe.
And you can safely delete the v0.1.0.
Whenever you download the new update (v0.1.1), unzip it, and drop your "saves" folder inside the "game" folder!
(Btw, even if you don't do this, I think your saves are saved automatically. But one never knows.)
You'll progress will never be lost!