So far we haven't been able to replicate these reports, what we expect has been happening is people have installed the game to a different path (accidentally). When they install the new launcher, it uses the default steam path and not whatever path the old launcher or beta version had set (maybe appdata).
What you can do, is use the launcher you have been using and check where the installation path is. Then copy the entire directory to your desktop or wherever as a backup, update and see what happens. If it overwrites, you'll have a backup. Please report what happens