Which storage areas can survive Deck updates?

So I had set up some stuff with EmuDeck and HeroLauncher on my primary drive, but it appears that some of it isn't working after applying an official Steam Deck update. So my question is: which areas of the filesystem are "safe" from being touched by a system update? I know Valve officially says "only flatpak applications are safe," so I'm moving over what I can to run from the Discover store, but not all applications are necessarily going to have a flatpak. Also, I'd love to be able to

I am also aware that, if not using flatpak, an application may use specific dependencies gathered from the system that might be updated by a Deck update, thereby making them no longer functional. I'm not asking about that aspect. Basically I want to which folders are exclusively readonly and which folders are possibly overwriteable by updates.

I looked around, but couldn't find this info. Thanks in advance to anybody who can answer some or all of this.