I don't think there is anything that you need to do, there is a thread here 🛟bazzite-helpSystem update failed. I think it's a key issue in github that the Bazzite/ublue team need to sort out.
Well, Flatpaks and basically everything; Distrobox containers, firmware, even Firefox GNOME Theme - but that's more relevant for desktop use. If you dock your Deck to use it as a computer it's a much more robust base.
I'm still very much a novice when it comes to Linux based systems. But I'm taking the challenge to daily drive it on my pc. And minus a few windows specific apps and vr, it's been smooth so I'll probably understand more in time.