Box2d bodies are not removed when scene is changed twice

In my game a had a collision listener when player touches the door.
Listener launched twice and door body was still collidable in new scene, yet its sprite was gone as intended.

Simple reproducer - click provided buttons a few times
https://github.com/Solidogen/retaining-bodies-bug

Start by running the reproducer at https://github.com/Solidogen/retaining-bodies-bug and repeat the scene change using its buttons. Trace Box2D body and collision-listener cleanup across the scene transition; done means the old door body is removed or non-collidable and the listener is not triggered again in the new scene.

Written by the indexing model from the issue text.