Another source of Aether (Spoilers?)

[Enkidoh]

Re-reading dialogue for that scene in question (via screenshots) she stated pretty clearly that it was key to forcing "Lahabrea to relinquish control of Thancred" (paraphrased) but exactly how it would do so was unclear, presumably using the aether in it to overwhelm Lahabrea's own actual Crystal of Darkness that he used to bind his will to Thancred's body and thus destroy the crystal (causing Lahabrea to be expelled from Thancred).

However, that never happened, as after the Ultima Weapon/Lahabrea fight, Hydaelyn draws both Lahabrea-in-Thancred's meatsuit and the player's character to Her, and the player evokes the Blade of Light to firstly force Lahabrea out of Thancred, when he's then dispatched by Hydaelyn evoking the collective will of not only the player's character but their allies as well which drives Lahabrea away (and ultimately destroys the Crystal of Darkness wrapped around Thancred's neck. At no time is the synthetic crystal ever shown and was never mentioned again.

So it's most likely something that was intended to be used but never was due to other means becoming available that were used, or at worst just a red herring.

Either way, this is the dialogue Minfilia mentioned about the synthetic Crystal of Darkness:

Minfilia: "Thancred's fate weighs heavily on my mind. I cannot bear to think of him in thrall to an Ascian."
Minfilia: "Mayhap you know this already, but the Ascians are immortal beings without physical form. Since time immemorial they have fanned the flames of chaos from the shadows."
Minfilia: "That they might work unseen, the Ascians entrap and possess mortal men by means of malign artifacts known as Crystals of Darkness."
Minfilia: "One such Crystal may yet be the key to saving Thancred."
(She pulls out a purple synthetic crystal, resembling a solid lightning crystal)
Alphinaud: "This is a Crystal of Darkness?"
Minfilia: "A mere replica, created using data obtained from anomalous crystals found across Eorzea."
Minfilia: "It comes to us courtesy of the Students of Baldesion, our distant allies."
Minfilia: "Even for an Archon, Thancred's talents are exceptional. We all had complete confidence in him."
Minfilia: "It was for this reason that none among us foresaw the danger in sending him to investigate the Ascians alone."
Papalymo: "Thancred had been striving to fill the void left by Louisoix. Yet it was plain he was overtaxing himself."
Yda: "Yeah... He would volunteer for everything and work til he was dizzy."
Alphinaud (thoughtfully): "And the toll taken by his exertions made him vulnerable to Ascian influence..."
Minfilia: "The Crystal that binds Thancred must be somewhere on his person. If we could but destroy it, his Ascian possessor would be compelled to relinquish control over him."