Did you try to rebuild the assy after changing the config?
For me, sometimes, the auto-rebuild is not enough to render the new model as it also depends on how complex the geometry.
If possible please check out your assy again and change config, then hit rebuild (the traffic light icon, or just use Ctrl+Q or Ctrl+B).
Tried that but it doesn't work. I have to open assembly and close.
I would have been fine if this assembly was its own thing, but it is to be used as a sub assembly in another main assembly.
Having to repeatedly do this is frustrating.
Here I have the assembly seamlessly switching between configurations.
As soon as I insert it into an new blank assembly and try switching configurations there it starts doing this.
But if I open the sub-assembly and close without doing anything its fine.