In the scenario I presented, it would not be necessary to insert a new layer, but the base layer itself that cannot be removed could be hide. And you can select an instance that’s on an invisible layer using the Instance Panel, but not clicking directly on it. But since you’re saying that there were no events that made the layer visible, then the images shouldn’t appear in the preview. This means that what I thought might have been your problem probably wasn’t. 
I’ve experienced an issue where some instances would suddenly get flattened and in odd places, but in the preview they show perfectly. It occours a long time ago and never occurred again. I don’t think it’s your problem, but here’s the thread I opened at the time: Scene editor showing instance in the wrong place
For now I don’t have any other ideas, but if I do, I’ll come back here in the thread!
Good luck. I hope someone can help you!