Remove a body from the game in AndEngine. This needs to be done on the updateThread. Code from: http://www.matim-dev.com/remove-body-completely.html

removeBody.java

final PhysicsConnector physicsConnector =
physicsWorld.getPhysicsConnectorManager().findPhysicsConnectorByShape(shape);

mEngine.runOnUpdateThread(new Runnable() 
{
    @Override
    public void run() 
    {
        if (physicsConnector != null)
        {
             physicsWorld.unregisterPhysicsConnector(physicsConnector);
             body.setActive(false);
             physicsWorld.destroyBody(bbody);
             scene.detachChild(shape);
        }
    }
});