Hmm. I'm wondering if it has to do with your water intake, maybe? Do you wake up dehydrated/overly hydrated? Or maybe your face is bloated in the morning. It could also be how you sleep on it perhaps.
In regards of eyes, our eyelids and how they rest on our eyeballs don't really change that much in our lifetime. Our eyelids placement mainly has to do with where the eyeballs rest inside of the eye sockets and so on. The small fat packet above our eyelid can be changed throughout weight gain or weight loss, and our eyes will appear sunken in the less someone weighs or the lower their body fat % is. But that doesn't make sense in this case.
It's probably not for concern but it's definitely interesting. I'm struggling to fully understand what you mean by disappear. Is it a dramatic aesthetic difference?