Ducklings can go through a phase where almost overnight they become terrified of people. Actually, of anything taller than they are. They also become frightened when they feel cornered or surprised.
This happened to my Runners. It was heartbreaking. And we got through it. BYC folks really helped me out with this. Spoiler alert: I have a very friendly, relaxed flock.
Advice I received - avoid cornering them. Avoid looming over them (I actually would approach the brooder, which was on the floor, on my hands and knees). Avoid surprising them - start singing or talking to them before you round that last corner and come into sight. Give them treats and sit as near as they are comfortable with, and just talk to them. You will need to toss the treats a little bit because they won't take them from your hand. Be extremely patient.
This process took weeks and weeks. But we came through it, and I even have a few ducks who like to hug, and most will calmly stand on my feet, or lean against me especially when I have treats for them. Some will cuddle up next to me if I take a nap in the pen. Yes, I keep it pretty clean, and I do put down an old towel for myself!