No, beta and live have two separate folders. Once Chapter 4 is out you can delete the beta folder.
I don't remember the folder/path exactly right now but it's something like ../Frontier/Products/Elite_Dangerous_x64 for live and ../Frontier/Products/Public_Test_Server_x64 for beta.
Ah ok, so: when 3.3 goes live, before downloading the patch I have to cut/paste the files from the beta folder to the live version folder overwriting the old ones.
I think the launcher does the copying for you. When you click Upgrade on patch day it will see that you still have beta files. The launcher will copy those and then download the files that have changed.
When 3.3 is ready to play you can go ahead and delete the beta folder.