Use the "Cache Management" feature in Yuzu (Tools > Manage Shader Caches > Delete > Rebuild). This forces Yuzu to rebuild pipelines while keeping your imported shaders, merging old and new data seamlessly.
Keeping your shader cache updated is a process that involves three paths: downloading from the community, transferring your cache to a new Yuzu version, or building it completely fresh. zelda totk shader cache yuzu updated