So, I don't know either, but here are my guesses. I can't reiterate how much this is just a guess and I am probably very, very wrong, but:
First of all, why would she do that? What kind of advantage would she have from that?
Enyo wants to give Amyntas back his memories to break his sense of hope and to show him the superiority of Empyrean. Alithea is convincing him to go towards war with Empyrean, and Enyo realizes the threat that Amyntas poses as the Emperor of Titans. She wants to make him believe that even if he were to turn all against Empyrean, he can't win. He has tried before, and he has failed. Anicetus is dead (or Enyo wants him to think), Acheron was destroyed, and their people are now nothing more than ashes of humanity stuck on the edge of a Cepheus Ring. Enyo made it clear that you either join Empyrean or you die, and the Seige of Anicetus was the moment that came true. She's giving Amyntas a second chance to reconsider and join the Empyreans, or face total annihilation, now knowing that he knows full well that Empyrean is superior.
Second: even if Enyo wanted to have Amyntas on her side, how could making him live again the Siege of Acheron make that happen?
I don't think Enyo wanted him or Alithea dead to begin with. I think Enyo wants her sister to rejoin her, and for Amyntas to obey.
Cepheon originally tried to wipe Amyntas' memories in the beginning of Proprioception before Alithea recaptured him and took him to the Cepheus Rings. They could have outright killed him, but they chose not too. I think it's likely that Enyo wants him alive so that she can use him, and the original plan was to wipe Amyntas' memory and reawaken him on Empyrean, possibly by only showing him the memories from the Soldier of Earth and not the Siege of Anicetus. Remember, when Amyntas awakens in [Cryostasis_simulation__2632_01], he initially has a very positive opinion of Empyrean. Specifically, take a look at the lyrics from Empyrean (song):
Fearless and free Fearless and free I have the right to remain The strength to sustain A life to regain We are fearless and free We are all bound to the sky For our birthright, stars had to die We will remain for eons Bound to the sky This final Empire This last Horizon
And these lyrics from Infineon:
A simple glance upward Is all I need To shatter the silence Of an apathetic breed Exceed the standards of our past The illusion of god has been exiled at last Fables once used to control Have faded away No need to kneel No need to fear A simple glance upward is all we need The past was bound by individual pride Only to be crushed by the weight of the sky Embrace the breed Of those who have been freed From the chains of this godlike disease
And these lyrics from Xenon (song):
From where I stand cities made of steel Cradle the horizon A global marvel gleaming with life From above the clouds
He's estatic with the progress Empyrean has made. It's not the hellscape he just left on Earth after seeing the Soldier of Earth's failures to reconquer the planet. If Enyo awoke Amyntas with just the memories of the Soldier of Earth, and showed him Empyrean, he'd likely join her willingly to ensure that paradise was protected. He wouldn't know how Empyrean was founded, only that it was worth defending as the Just City. He would probably assume Empyrean was just the continuation of the survivors from Earth.
Alithea stopped Enyo from doing this when she retook Amyntas. She convnced Amyntas to rebel in Cepheus:
My origin falls from the tip of her tongue A soft spoken declaration of war
And in Xenon (song):
Why has she instilled this disdain toward such awe With her soft spoken declaration of war She whispered to me [Bring this world to its knees Let them reap what they sow War and disease]
And in Terrea:
[Utopia is only a dream Make sure you never forget that]
By showing Amyntas what Empyrean had done to Acheron and how the Empyreans were treating their human population, Amyntas became convinced that Empyrean needed to be destroyed. At the end of Xenon (album), Amyntas has vowed to follow Alithea and destroy Empyrean. Enyo has likely realized he's awake, realizes that Alithea has likely convinced Amyntas to destroy Empyrean and now wants to convince Amyntas that although he believes he should destroy Empyrean, that he either can't or shouldn't.
Now, how could Enyo go on the Cepheus Ring, amidst the Acheron survivors, without Alithea knowing it and preventing her to have a contact with Amyntas?
Enyo and Alithea are twins, so the timeline likely goes like this:
1. Alithea recaptures Amyntas, and they go into cryosleep in Acheron:
2. Amyntas is reawoken, and Alithea takes him to the surface of Empyrean to show him the planet. See this line in Alithea:
I will see what world lies beneath me Holding on to a fading dream Of a world that may be the just city Holding on to a fading dream That this world may be Just may be the Just City
3. Amyntas goes on his own to Acheron, and Alithea and Amyntas split. See this line from Phedra:
I will breathe the air of Acheron to see if it tastes of earth
4. Enyo goes onboard the Cepheus Ring, posing as Alithea. Remember, even Amyntas didn't recognize that it wasn't Alithea, it's likely the remaining inhabitants of the Cepheus Ring wouldn't recognize Enyo as anyone but Alithea either.
5. Alithea then races to reactivate her Titan Daedalus in Invictus Daedalus, realizing what Enyo has done and where she is, suspecting something is about to happen.
As to whether we get a Xenon sequel is up to Joe, but personally, I'm guessing we have one more prequel or a single song like To Coexist Is to Surrender or The World We Lost that fills the gap between the founding of Empyrean and the destruction of Acheron.