Three mysteries of the island are related to elevation above or below sea level.
- The Black Rock slave ship goes from being in the water to being "in the middle of the jungle" in an instant, to the mystification and dismay of her crew.
- Ajira Airways Flight 316 inexplicably appears at island-top altitude, despite having been at cruise altitude (typically close to 40,000' above sea level) moments before with no recognizable plunge or emergency descent.
- In the first part of the Season 6 premiere, the island itself is below sea level, but otherwise intact.
I was going to accept the Ajira drop as a combination of typical movie ignorance of airplanes and dramatic exigency. The island would be barely visible to an airplane in cruise, and if an emergency descent were commenced directly over the island, the airplane would be at least 35 miles beyond it by the time it was at the level of the peaks. It's true that if the airplane was under the influence of the island, then it couldn't leave by flying straight ahead, but the scene doesn't imply a five minute rapid descent, just pilots flying in turbulence and then suddenly and unexpectedly seeing a mountain peak appear in front of them. There was no physical sensation of changing altitude. They were just there. The conclusion is that the island instantaneously transported the airplane to a lower elevation.
The Black Rock's situation high and dry in the jungle has been an oddity since we found out that its name didn't refer to a geologic formation. It seemed to be up in the hills in the episodes when they went there for dynamite, but it isn't too far a hike for Ricardo from there to the beach. But as he's presumably been back to see Jacob many times over the last 140 years, but never to the wreck, it's a decent ways away and not on the obvious track. The man who kills the other prisoners in the hold says that the ship is in the middle of the jungle, not that it is run aground, and Ricardo needs directions from the MiB to find the beach. The Man in Black also tells Ricardo that the ship crashed through the statue into the jungle. We see the detritus of the statue on the beach when Ricardo reaches it. How tall is that ship compared to the statue? The statue has a fairly high base and its knees are well above that. A ship in the water would plough into the base. While yes, if the statue were unstable to begin with, hitting the base really hard might cause it to crumble, the base is still there, so the ship didn't fly through the base. The ship must have hit it above the knees in order to fly through it, and the damage to the statue is a lot more consistent with that sort of hit. The ship flew through the air in the way that normal ships do not. We don't see the prow of the ship, so that may be destroyed, but the hold of the ship is not destroyed, not even splintered enough to free the slaves, and the vessel is even right side up, not on its side the way a ship should be if it were dropped. My conclusion again is that the island lifted the ship into the air and then lowered it into place.
In both cases the crew is disoriented by how their craft has reached that point. In the Ajira case it appears that the transport has taken place during the white flash. No white flash is evident in the transport of the ship; the lightning flashes are distinct. But there is a cut and a night-to-day transition between the ship at sea within sight of the island and the ship aground. The actual grounding is not shown, and I think it is implied that the crew is unconscious and all wake up to find themselves in the middle of the jungle.
I don't actually believe that these events and the lowering of the island below sea level will turn out to be connected by The Great Island Elevator, but this sort of implausible connection is what blogs are for.