if it's what I think, you're not alone with this issue, in my case just giving the power button a tap and letting it shutdown on its own and rebooting seems to bring it back
Depends on what you want to do. I like Bazzite for desktop because it's container based, an update will never ruin your system, and has batteries included (like updated graphics drivers)
For general use, most applications are available as flatpaks, Steam and Lutris are there for games. If you need a more in-depth system, Distrobox is there and is very tightly integrated to the point where I forget it's not the base system sometimes
Nested desktop has been removed in the latest fedora 40/Bazzite 3.0 update, as it's not fully supported there yet. More about it in the latest Bazzite Buzz