The OnePlus 3 is protected by Corning Gorilla Glass 4. So the dust (in theory) should not scratch the display at all. Obviously, just be careful and don't force or push things. The tempered glass may crack if you remove it but at least you will have removed the dust from the screen then. Hope your phone goes back to being all clean again.
People have reported that dust scratched their phones so it is possible. Especially if it's really fine dust. Gorilla Glass 4 is pretty good at stopping scratches but not invincible. If you are careful, you should be fine.