Ah, I think I see part of the confusion here.
The shards themselves are more akin to 'parallel dimensions' than 'parallel timelines' (think more Chrono Cross than Chrono Trigger). When Argos sunders himself, he produces multiple identical copies. The same is true for the shards of Etheirys, except that their histories diverged about twelve thousand years ago, such that there are similarities and differences to each. For example, Norvrandt, the part of the First that survived the Flood of Light, is essentially just Eorzea. Eulmore is Limsa, Rak'tika is the Shroud, Amh Araeng is Thanalan, Il Mheg is Ishgard, and Lakeland is Coerthas. There are differences of course, to account for our different histories. Midgardsormr used to sleep by the aether rich waters of Lake Silvertear, entwined with the wreck of the Agrias. Bismark instead sleeps in the aether rich waters of the Source on the First. There's very much a 'Light World'/'Dark World' vibe in this. I'm pretty sure that I turned into a rabbit when I first arrived in the Dark World.
How the shards influence each other hasn't been clarified yet, but that's the really interesting part. The main relationship between them is likely the lifestream. Why is it, for example, that an event that wipes out all life on a shard causes a rejoining? If the lifestreams are all connected, then perhaps the souls all just migrate back at the same time, the force of which pulls the two shards together. There's also the question of how the elemental alignment of the shards are linked. For example, Mitron explains that when the Ascians brought about the Flood of Darkness and transformed the Thirteenth into the Void, the shard that was most influenced by this was the First, which strongly shifted its polarity towards the Light. Which is why the First is actually the Shard that the Ascians were trying to rejoin for the longest. So why is it that the First and Thirteenth have such a close relationship in particular? And if so, what other pairs of worlds have a similarly close association?
This is the sort of thing that I really want to understand with regards to this game's dimensional travel.
The timelines are different in that they represent 'possibilities'. So each timeline in which the sundering exists should contain the various shards simultaneously. When Dayan meets Mide in the mathematical simulation generated by Alexander's core, he explains that Alexander's creation generated an infinite number of potential futures separated by 'nary a thread'. Each one represents a potential outcome across all the shards. In one of them, for example Alexander prevents the Seventh Umbral Calamity by punching Dalamud out of the sky. In that timeline, the Seventh Shard still exists. In all other timelines, it doesn't. Likewise, in the Eighth Umbral Calamity timeline, the First no longer exists, while it still exists in our timeline.
The short story 'Tales from the Shadows: An Unpromised Tomorrow' seems to suggest that these individual timelines are completely disconnected from each other once the 'flag' event has passed. When Biggs III and his team transported G'raha back in time, the Crystal Tower disappeared from their skyline entirely. The implication being that they couldn't backtrack into our timeline. There is of course the question of what happened in the time between the Warrior of Light's death and G'raha's departure from the Eighth Umbral Calamity timeline. You still have the likes of Emet, Elidibus, Hermes, and Meteion floating around. But I think the main point of that story was to show that humanity would find a way forward on its own, even without the Warrior of Light's interventions.
'Though we shall remain forever on different pages of history ─ and different books, besides ─ I take comfort in knowing we strive for a future of the selfsame brightness.'