SteamOS installs seem to have a flag that determines if they have ever been booted or not. (in the hold '...' button menu, they just show up as 'Previous B' instead of 'Previous SteamOS-B-...'), and when booted will do something that actually downloads SteamOS and installs it proper. It seems however, when one of these not-quite-fully-installed-SteamOS boots up, it erases the Steam install directory, along with all user settings, installed games & save files, without any confirmation from the user.
Now, it's unlikely an average user would run into this (I think you'd only be able to do this by doing a reimage, and then copying files back onto the Deck before booting for first time, or if the user uses the '...' boot menu to boot into a secondary B partition, when no secondary partition is present.), but its still annoying that my Deck just wiped my games without asking