Doesn’t each separate .exe you add as a non-Steam get its own proton prefix? That is, each of them end up with their own [random numbers] folder that doesn’t match another?

and chose the C:/Program Files (x86) as the install location

This might be the problem, but I’m not sure. When you choose C:/ as the install location in the installer, that C:/ is inside the proton prefix of the installer executable. I believe you’ll want to choose a place outside of that. For example Z:/home/deck/Games/Genshin Impact or the SD card like the guide was showing.

I’m guessing when you deleted the installer.exe from your games list, it removed the proton prefix for it, deleting the game you installed in there alongside it? Either way, from a quick glance that’s what I could see you did differently from the video guide.