Simply download the new version and click "Continue". There are no extra steps required unless you're using Android.
But where game progress info is stored?
The FAQ in Discord has info on save file location by platform.
I have to download new version into same directory by replacing files?
You do not have to do that. You can, and it may work.
Or It stored somewhere in cache so i can download new version into separate folder and still keep my progress?
It is not a cache, just a directory outside of the installation directory tree.
The Wiki has a FAQ page, which nobody seems to read.