Just like we do today, ancient advanced civilizations would have created underground bunkers in order to survive a catastrophe.
If such an event happened in the ancient past, the existing advanced beings would have sought refuge underground (much like we would today).

Having experienced a massive disaster the earth would then become uninhabitable for the ancient beings. Forcing them to stay underground until they could (if they could) return to the surface.

And what happens to life when devoid of light, cramped in a smaller environment. The skin loses pigment (grayish color), the eyes become large to adjust to no light (large and oval), the body would not grow tall due to a smaller (enclosed) environment (around 3-4ft tall).

Sound familiar? That criteria fits almost every alien sighting ever.
Maybe that's why we here about massive UFO sightings at night and not during the day. The old ancient beings cannot come out in the sun.

They sit under the oceans and the earth. They have had tens of thousands of years (if not hundreds of thousands) to develop advanced technology that surpasses ours by eons.
We think they are coming from space when they are not. They may travel to the moon or mars for resources but by no means do they come from outer space. They have been here the whole time.
They built the ancient megaliths. They built civilizations in the past. They taught the ancients everything they know.
It's their world, we are just temporarily inhabiting it.