OK, so, as far as I understand it:
Firstly, a shader is a text file that instructs a computer's graphics card as to how to render objects. Without shaders, games wouldn't have lighting, shadows, screen space ambient occlusion, bloom, etc. When a game renders an object onscreen using a shader, it has to compile the shader first. Doing this live can make the game stuttery - however, with Proton, Valve is taking these compiled shaders, caching them to a file, and sharing them with other similar graphics cards / GPUs (i.e. between all Steam Decks).
Secondly, the shader cache gets updated when a new shader is encountered and compiled. This means that when you download a game, for example, you'll probably also have a download consisting of the compiled shader cache for that game. However, these caches are based on shader compilations that happen when a shader is encountered in a game. If nobody encounters a shader, it won't get compiled and cached. As more people play a game, the cache gets more and more complete, and so fewer and fewer people should run into stutters where a shader is used that is not cached.
Being that generally few people have Steam Decks, shader caches are mostly incomplete - once more and more people have Decks, cache downloads should become less and less frequent and more and more complete, as more people are playing any given game (and so they are happening upon shaders more regularly) and everybody contributes to the Deck's overall cache.
I don't believe the cache is invalidated on graphics settings changes - the shaders are most likely compiled regardless of personal graphics settings (as most shaders are the same regardless of if, say, the resolution is 720p or 4K, and which is why you'd have a shader cache to mitigate stuttering even before you start a new game).
The cache may be invalidated on graphics drivers updates, not Proton updates, as far as I know.
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