On the steam deck go to Settings > Downloads > Enable Automatic Updates. That should download the updates as soon as they are pushed onto Steam
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While this works, it can be pretty detrimental to game performance to be updating in the background.
You can also just enable background downloads for specific low performance games, and play those while you wait on downloads.
Leave the deck running, steam link into it from your phone when you leave work and start any pending updates.
Im afraid I don't have a solution, but I share your pain friend. Sometimes I can only squeeze in an hour of gaming, fire it and argh update time.. Maybe tomorrow 😞
Is it possible to leave the thing powered on, and trigger the updates on a schedule, or remotely?
You should be able to enable download while a game is running
If it's shaders, you could potentially turn off downloading shaders in desktop mode. I don't actually know if things are a Stutter mess anymore after many changes in 3.5 if you do that. (That async stuff)