From On the History of the Sunstone, by Glowing Hope:
Our earliest knowledge of the Sunstone comes to us from circa the 2nd century BE, when the unicorn knight Gusty the Great writes,
"The vile witch Hydia and her daughters have recently contrived to darken Flutter Valley and conquer it for their own with the aid of the large bees who live in the nearby Forest of Ice. To this end, they promised the Sunstone to the bees to bring warmth and light to the Forest of Ice, so that the bees could grow their own flowers once again. The witches themselves seem disinterested, even disgusted, by the warmth and beauty of the sunlight; they seem to wish only to be rid of the Sunstone and therefore gladly see it as a convenience to be able to offer it to the bees. Their only object seems to be the desire to corrupt and twist Flutter Valley, for the perverse pleasure of tormenting the flutterponies who dwell there. My companions and I stopped Hydia, by means of fortuitiously made alliances with the creatures who dwell near Flutter Valley. The bees and the flutterponies have reached an accord to share the nectar of the flowers of Flutter Valley, ensuring alliance and a lasting peace between them."
Gusty writes again, evidently some years later, but the precise dates have been lost:
"Once more Hydia, that vile witch, has made an attempt on the Sunstone. She devised strange magic, seeking to siphon away the Sunstone's power into a surrogate vessel. There were no local soldiers available to deal with the emergency of her latest act of aggression, and so I hired the most capable among the general populace in the immediate area to make an attack upon her castle. I have many reservations about hiring mercenaries, let alone amateur mercenaries (my misgivings were justified when one of them tried to walk out of the castle after helping herself to an alarming amount of dangerous alchemical flume), but the stakes were high and the cost of inaction too great. The magic Hydia used was unfamiliar, and unsettling in its apparent sophistication. I believe it to be well beyond her usual capabilities. Why she attempted to do this when she never wanted the Sunstone before is also as yet unclear. What I gather from the adventurers who defeated her is that one of her daughters was infected with the flume-plague, and also that Hydia was heard conversing with someone possessing a voice with the character of a goat. It seems possible that Hydia was serving the purposes of another malevolent creature, perhaps in return for her daughter's life. In the end, the infested daughter was turned to stone, and Hydia escaped through one of her portal-paintings, presumably back to her native realm. We have destroyed the paintings to the extent of our ability to find them, having conducted thorough searches of the castle. May she never again trouble us here!"
So it is clear that the Sunstone was known to the classical era, and predates the coming of Celestia and Luna. Thus, the stone was not, as some have speculated, created by Celestia, but rather--
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The Sunstone seems to have resided peaceably in Flutter Valley until the year 1027 AE, when Queen Glitter Dew writes,
"Disaster! The Sunstone has been stolen from us by a pegasus, Sunsparks Twinkle. She feigned interest in seeing it as a tourist, to get close before deploying devious magical devices the like of which we had never yet seen to overpower the guards and wards and seize the stone for herself. The poor creature was clearly unhinged: I discovered she had a pyromanic history before she even came to us, but went utterly mad with the power of fire the Sunstone gave her. It was horrible to see! She burned alive the guards who rushed in close to stop her, and thus unopposed, began to set the vegetation and structures in her vicinity to the torch. What terrible waste. There seemed no better reasoning to any of it than her enjoyment of the flames. In the midst of her rampage, a mysterious creature with dark, spiraling horns approached her. They appeared to have words, and then to fight. As they struggled, Sunsparks used immense and intense fire, which the other creature could not endure and was forced to flee. Before the fight was finished, the strain of it caused a small piece of the Sunstone to crack and break off. This lesser piece was, we believe, seized by the fleeing creature and has never been found. Her long rampage destroyed much of the habitable structures of Flutter Valley. At last, answering our calls for help, a wiley unicorn mage was able to get close, and through feigning curiosity and promises to show Sunsparks more secrets of the Sunstone's magic, struck quickly enough to kill her. But even with the poor creature out of her misery, the damage was not finished; upon examining the remaining piece of the Sunstone, we found a dark, lingering curse within. Its magic is intact, more or less, but fearful to use. I haven't fortitude to withstand that burning glare, the malevolent face of Sunsparks Twinkle, Village-burner and Orphan-maker, that gazes out now always from within. It will take somepony of immense skill and great power of both magic and will to cleanse it, if ever it can be. Our hopes have died and my people are caused great hardship. I fear for their future, and I do not know what we will do now."
After 1027 AE, history records that Flutter Valley grew cold and dark. Its rich fields died and the flutterponies dispersed to the four winds, settling far and wide among other pony types. Their bloodlines are not wholly extinct, as their descendants were brought into the fold of the other three primary tribes, but not for centuries has a flutter pony been born. Such was their degree of dependency on the Sunstone; its loss was tantamount to the loss of the whole race.
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--at which point the Sunstone was committed to the royal reliquaries of Canterlot, wherein many such dangerous artifacts were kept safely contained. These reliquaries were generally considered the safest possible storage for items like the Sunstone, until the Catastrophe and its accompanying general decline of order and authority left nopony clearly in charge of the responsible custody for--
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--arrived at Sunshine, and was brought to the abbey. Here it has been kept closely guarded, the means by which cannot, of course, be discussed--