Or just have a different ball ready to come out of the exit hole, the top hole would swallow ball 1, and a different ball could exit after a realistic delay...

A bit like Star Trek teleportation.. is it you, or a copy of you?

Several real pinball tables do this, keep a hidden ball staged to make it seem to instantly reappear. The Rick & Morty machine in particular does this - you can shoot into a portal, and the ball (actually a different hidden one) reappears instantly some distance away.