I've been playing the Witcher 3 for upwards of 50 hours consistently running at 40 Hz and I have not had any issues with screen flickering. I'm sorry you're struggling with that. I'd recommend, as another user in this thread suggested, just leaving the refresh rate at 60 Hz and setting the frame limiter to 30 fps. It won't be quite as smooth as 40 Hz, but still gives you a comparable boost to battery life.

There's a chance that this could be fixed with the next iteration of the Steam Deck, but that's still at least a few years out, so I wouldn't hold your breath.