Updates do not apply to deconstructed ROM directories (folder with main, main.npdm, game.romfs, etc).Don't be alarmed if the numbers don't match what the game says the version is, the version in the game list is the version as determined by Nintendo's servers, the one in game is independent. If you copied your NAND or SD or used an NSP update, it will probably say Update vX.Y.Z where X, Y, and Z are numbers.If you installed just an update NCA, it will probably only say Update.If your update was installed successfully, next to all games that match the title ID of the update, a message will show in the add-ons column of the gamelist.If your update is in NSP format, use the File > Install File method described above for NCA, except the Game Update menu won't show (yuzu can infer it from the NSP metadata).If you have updates installed on your NAND or SD card, you can copy the entire NAND into %YUZU_DIR%/nand/user or the entire sd card to %YUZU_DIR%/sdmc.
If you get an error, double check you encryption keys and dump. This is because newer version uses newer Switch OS features we haven't implemented. NOTE: At the time of writing this, most updates to complex games don't work.