Fallout 4 Loses Graphical Options on Steam Deck From "Next-Gen" Update - Steam Deck HQ
steamdeckhq.com
Fallout 4's next-gen update is out now, but unfortunately, it seems to get rid of the graphical options on the Steam Deck.

Fallout 4 just got updated with a “next-gen” update that got the game Steam Deck verified, fixed bugs, and added some new content.

However one of the ways they got the game verified was by disabling the game’s launcher by default, the same launcher that is the only way to change graphical settings.

You can re-enable the launcher by changing your steam launch settings to SteamDeck=0 %command%