How to substitute flour with nutritional yeast
I think this is not such a good idea. It is going to take a lot of nutritional yeast to get anything like the thickening power of flour. If you really want to thicken this with less flour, there are plenty of other things that will do the trick, like xanthan gum, potato starch, corn starch, ultra-tex, some formulations of methylcellulose, etc. Just add however much nutritional yeast you want for flavor or health reasons, and get your thickening elsewhere.