Doesn't sound like a dynamic component or geolocation issue if it is removed by save and reopen.
Perhaps you can record it to gif or vid next time it happens.

If you view in Monochrome mode are you sure the material is applied onto a 'front'.
If your Style has a distinctively back-face color versus front-face then you'll see it clearly.
Most renderers do not render back-faces, even when they have a material...

PS: Posting a simple example SKP would also help us help you...

Well, I hope you're right and it doesn't happen again. That Ctrl X would cut the selection to the clipboard where it would still be available to paste until you hit Ctrl C or quit SketchUp. Still, it's worth paying close attention.

Good luck.