If you have a portable installation (config inside install directory) and Yuzu is installed in a directory that requires elevated permissions to write to (C:\Program Files), then you would need to run Yuzu as administrator in order for changes to stay OR you would need to move the Yuzu folder elsewhere.

Otherwise, if your install is non-portable (config somewhere in C:\Users\username\AppData) the file you are trying to modify may be set to read-only (check properties from right-click menu)

I'm not at my PC to check/verify any of this, I just happend to see this while browsing. Hope this helps.

This happened to me when Yuzu sometimes didn’t recognize my controller. My controller was connected via Bluetooth, and it showed up in BetterJoyForCemu, but it did not show up as an input in Yuzu. If I selected some saved configuration, Yuzu would see that all of the buttons in that configuration were from an input it didn’t have listed, so it wasn’t able to actually switch things to that configuration.

For me the fix was updating BetterJoyForCemu to the latest version and making sure I had my controller connected to BetterJoyForCemu before opening Yuzu.

Not sure what your setup is, but my guess is that Yuzu either doesn’t recognize your controller as an input, or it doesn’t recognize it as the same input as what’s in the configuration.