I replicated your multi scene sample with the same structure, empty loader scene with the scene loader component that references 2 scenes. This empty scene has the needle exporter in it and a needle project set.
The 2 scenes each have a camera with orbit controls on it and several gameobjects with a button component on them. On click is set to trigger orbit controls => SetLookTargetPosition and reference to the clicked GO. The following happens on click:
In the needle inspector on chrome the scene turns inactive and the camera transforms is NaN. Sometimes I also had the browser console to print either the NaN issue or that the referenced GO is not an actual gameobject.
However if I set either of the 2 scenes as their own projects and export and load them on their own, the click and SetLookTargetPosition works like expected. Only the scene loader setup causes this issue.
I also tried giving each scene its own exporter and seperate needle project but this did not fix the problem. Something happens to the orbit controls when a new scene is loaded.
I also tried to add this button and orbit control call in the multi scene sample and its the same error.