How do you update the emulator without losing any data again?

rpcs3 always had dev_hdd0,that's where your games are(unless you modify the dev_hdd0 path from the settings)
The archive you don't don't contain anything settings related so you can just extract the archive into your rpcs3 folder,you will not lose any data

What I do when I update is downloading the archive,open it,select all of the files and only the qt folder and drag drop them to the rpcs3 folder and overwrite all.
I usually rename the old rpcs3 exe just in case this new build contains a bug that break some of my games so I know to what rev to return to while waiting for a fix

I have never lost any data while updating rpcs3 almost every week since I started using it,more than a year ago