If you look closely, he uses a couple of frames for him to disappear, what hes using is getting the stickman, and putting the eraser at transparent, so that the stickman sort of fades. He copied the image of the transparent stickman and pasted in onto a layer, as it intercepts with its counterpart, creating the effect of an afterimage, and then, the stick man disappears.

The stickman and his surrounding environment including the other stickman are separate layers, thats how he pulls it off.

I cannot help but admire your genius effect, it looks cool!