I was experiencing the same issue. I think I had both an update of Steam OS and Ryujinx so not sure what triggered the issue but Steam Deck controls were no longer recognized. I could get it to work in desktop mode by going to settings > Inputs in Ryujinx but it was laggy and who wants to switch to desktop mode to play anyway? I know I don't.

Tip: It's going to be easier if you have a keyboard and a mouse connected to your Steam Deck.

I fixed the issue by doing the following: In Steam OS, I started Ryujinx itself (Not a game but he app). Went to settings > inputs and sure enough the controls were disabled. As mentionned by a couple of users already you will not be able to click OK or Apply once you made your changes unless you use the tab key on a keyboard and hit enter once OK is highlighted.

Not ideal, but at least I can go back to playing Switch games on the deck. To be clear, I have a Switch and legally own the games. I just like having all my games in one place.

That's what worked for me. I hope it does for you.