It's gonna take more force than just "pulling up" on the bolt. If you can get a pin punch through from the other side (nut end) give it a good whack to distort the clip/nut. If not wedge under the square of the bolt to engage the nut. Those nuts (also called tinnerman nuts) are stamped steel and distort when the fastener is tightened. They don't require "good" threads on the bolt for engagement, but the edges of the nut do need to engage a thread- which is why they must be forced into shape.