I think for your use case you should consider skipping the Unity plugin and export your models in a typical model format (.obj or .gltf). This way you can drop those objects into Unity or Blender, start to pull apart the materials like you want, and build your Unity project to VR world.
Our plugin for Unity (i believe) is meant to be an editor only tool. When you build something for VR world, or any other type of Unity thing, our plugin will get stripped out of your Unity project along with any other editor based tools so we would expect that you would get these errors since you are created a standalone build while still trying to access our removed plugin.
The issue you’re getting with the model disappearing after you remove the files also is expected. Our plugin for Unity is a bit different form our others as it places the models in your scene through a data stream rather then downloading locally… Actually, I’ll need to double check that one… However, when you remove the files from Unity the Arkio plugin will break and flush out any of those streams you have of those models.