Bar is way too high -- these are not low bar back squats. Review bar placement in the SS book and videos.
Your squat is also too high -- you aren't breaking parallel, and in most reps you aren't even close.
Fix your bar positioning and thus get more horizontal with your torso and be sure to break parallel on descent, and then you should find your hips and glutes engaging more properly, taking stress off your knees.
I was also going to ask why on Earth you would deload 20% just because of one missed set ... but if you aren't getting deep enough you probably need to deload and work back up with a proper squat anyway.
Keep at it, and good luck.