Settings of apps installed via Discover are stored in /home/deck/.var/app. Settings of the desktop and pre-installed apps including Steam are stored in /home/deck/.config and /home/deck/.local/share.

For backing up I wouldn’t bother much with differentiating between stuff I want to keep and stuff I don’t. I’d back up everything in my home folder with sudo rsync -avP /home/deck /WhateverTheLocationOfTheDriveIs. Let the Deck format the drive for you and then this command will copy the whole deck folder over and preserve all permissions. You can start it over if you get interrupted for some reason and it will pick up where it left of.

I’d only worry about what to copy back when setting everything back up again. But I probably would just start everything from scratch to get rid of garbage.