Unfortunately I haven't had time to read through all the stories here, so I'm asking the devoted fans for help.

Has it ever been adressed where Luna and Celestia came from? I've got my own theories, a half-formed story (that has been driving nme insane since it first came to my mind,) but that's kind of a major part of it.

What about the Crystal Empire? Specifically, its fall? Has that ever been mentioned, and how all of that went down?
What about its new rise? I seriously doubt it only took a day and some prancing around to fix the entire empire. For that matter, is the CE in the Winningverse really just a city?

As far as I can tell, none of these questions have been answered to any real capacity. I mean, no one's done a fic directly involving Celestia or Luna as a main character, and the only fic that's even tangentially related to the Crystal Empire is In the Service of the Princess, which stars Flash Sentry but so far takes place outside the Empire.

None of these questions have really mattered enough to any of the current stories presented in the Winningverse to be delved into in any real capacity to date.

To answer a couple of those:

1 Lunar Rebellion mentions a little bit about their origins. Celestia and Luna were born into the Unicornian Royal Family, but eventually discovered a way to tie their powers and life force to the sun&moon, giving them their godlike power and immortality.

2: The Crystal Empire originally had more territory, but only the capital city got pulled into whatever spell Sombra used to lock it away, and without a clear leader or ruling class the rest fell apart pretty fast. Equestria absorbed most of the Empire former territory, with the rest going to the caribou, yaks, and whoever else is up north. I expect running it is a bit of a pain that keeps Cadance quite busy, and it can't really get its old lands back since new inhabitants have moved in during the time the Empire was locked away.

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With the recent addition of Yakyakistan in the season, I'm working on formally introducing the such tension between Rutherford and Cadance in a future installment.

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Out of curiosity, does that mean they're actually both moral Alicorns who've created phylacteries out of the sun and moon?

If you take the show as cannon, there is no real history for Celestia and Luna. The closest (or oldest) history shown is two scenes from where they first petrify Discord. Physically, they are the same as in the 'present' time, including their jewelry, except a little roughed up; probably from their search for the Elements of Harmony. This would also indicate that neither are aging in any significant fashion.

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No, the connection isn't like a phylactery. Their souls are still in their bodies.

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I was considering having some of my own fun with that. In addition to other issues the Crystal Empire might have with its neighbors.

4885031 I imagine trade being one of them? With most of its territory gone and Yakyakistan on not-so-good terms with it, the CE has to do a lot of importing, which more than likely puts a dent in its funds. Then again, the crystal ponies seem well off thanks to abundant sales in crystals. Especially the sky blue ones.

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Trade would be an issue. For one, cities are rarely wholly independent once they get to a certain size, and need food and other resources from neighboring areas in order to survive. There is also the fact that the Crystal Empire is going to be a thousand years behind in economic advancements, and I'm going to guess that Sombra turning the CE into a slave economy didn't do great things for economic output and prosperity, either. So likely the city's economy is an absolute mess that's either going to take a long time to recover or require a lot of aid from Equestria to pull out of.

There is also the fact that it's unlikely that every crystal pony is going to be in favor of being annexed by Equestria. They had remained independent despite the other pony tribes uniting under one banner, and there were probably reasons for that. National sentiments not being one to ignore. And now Equestria has installed some foreign princess on them. At least from my readings of history, not everyone is going to be on board with the new order of things.

There are also the old elites of the Crystal Empire to consider. This gets into headcanon, but there would have been power groups within the Empire before it dissapeared. There might be remnants of the old royal family, a nobility, guilds, and old flunkies of Sombra's.

Then a lot of crystal ponies are not going to be happy about losing so much territory, and some might want to reclaim at least some of their former glory. Add that to the issues of being annexed, having a foreign princess ruling over them who is unlikely to do anything aggressive, and having neighbors who might not be happy to see the revival of the Empire, and you potentially have a boiling pot worth of trouble.

4887392 Cadance is said to be a descendant of Princess Amore, the Crystal Empire's ruler before she got crystallized and splintered by Sombra. If there's a blood relation, however distant, between the two, it may have the idea of Cadance being their empress be somewhat more appealing, at least to the nobility and fanatics, and therefore ease unrest to some degree between them and their new rulers.

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Was that stated in the relevant episodes in the show? I know that's certainly been something thrown around in the fandom, and maybe the comics, but I can't remember it being stated in the show.

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Cadance is merely a pretender to the throne. Behold, the rightful heir to the Crystal Empire and the Crystal Heart!

But honestly, if Cadance is the descendant of Princess Amore, it raises many more questions than answers.

4887530 Not in the show, no. It was stated in the Journal of the Two Sisters written by A. K. Rogers, which is as close to canon as any of the books will be (aside from Barrow's entries), and expanded on in the comics coughnotcanoncough

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Like how an orphan pegasus raised by earth ponies, who later was adopted as a niece an alicorned by Celestia, is the current co-ruler of the Crystal Empire and just happens to be a descendant of its last ruler, who has been not-quite dead for over a thousand years? Hell of a mind-boggler, but all I can say is, and to quote Xehanort, destiny is never left to chance. It is how it is.

Which reminds me, will Lyra's ancestry with the Empire be further explored in Symphony, or are there other plans for that?

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expanded on in the comics coughnotcanoncough

How can a single comic do so much good and then be so bad?

Shadow ponies/Umbrum? What a terrifyingly good design.

Sombra's backstory? What a terrifyingly bad idea.

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Which reminds me, will Lyra's ancestry with the Empire be further explored in Symphony, or are there other plans for that?

Probably not, given the events of Symphony take place in Season 2, so Lyra's blissfully unaware the crystal empire even exists. I'd have to work up another fic to explore that.

A certain long lived character may make reference to her ancestry though...