SPOILERS - I have questions about calamities and the order of events from DT

[Layte_Aeon]

There are perhaps 2 things to keep in mind.

Firstly, all talk in game about the Lalafell escaping to a different shard is phrased as speculative, as there is currently no way to prove that hypothesis. Even when Y'shtola looks at the big gate she can only presume it leads to another shard. It wouldn't be the first red herring we've had.

Secondly, shards are alligned not just by element, but by polarity. That's how the First and Thirteenth can be aspected to light and dark, or passive and active. As such there would still be another lightning aspected shard that the Lalafell could go to.

[Alenore]

Firstly, all talk in game about the Lalafell escaping to a different shard is phrased as speculative, as there is currently no way to prove that hypothesis. Even when Y'shtola looks at the big gate she can only presume it leads to another shard. It wouldn't be the first red herring we've had.

The gate Y'shtola mentions say it leads to another reflection because it's pretty much similar to a voidgate, on top of a whole area merged by interdimensional fusion. The entrance to the City of Gold leads to the same place sicne Krile's parents were from there and build using the same material and technology.
As for where the Lalafell moved from : no way to prove an hypothesis, but there's conclusive arguments they were from the Source. Given they used an artifact meant to do interdimensional stuff, and moved from a world imbalanced toward Ice (warm sea freezing during the course of a lifetime? Unlikely.) to one Lightning-aspected is enough to conclude they did switch dimension.

Krile: For an event that froze the seas, the Fifth Umbral Calamity comes to mind─that which ushered in the Age of Endless Frost.
Krile: And legend holds that, during that age, the entire population of the south sea isles vanished overnight.
G'raha Tia: The art of arcanima, too, traces its roots to the calculations of the south sea islanders. While we cannot outright conclude that these people were the Milallas, there are at least enough points of similarity to support the theory.

It's also worth noting that...

...the lightning disaster that hit Sphene's shard cannot have caused it to be rejoined, as she mentions that the dome was constructed after that point.

That's not to say that it couldn't have been rejoined at a later point in time, but that would make the timeline even more convoluted. I suspect it's more likely that this is just another shard that happens to be lightning-aspected, not the Twelfth.

We're literally going to Living Memory, so the shard still exists. and the gate at the top of the eleventh level of Solution Nine, where we fight Zoraal Ja is a gateway to her original shard, since there was no Interdimensional Fusion before he used the artifact.
It was merged from somewhere that still exist, somewhere we can open a portal to, and somewhere we walk around. So pretty much not rejoined.