I figured the Red Crystal was used up after transforming Enraged Sue into her form. It had already saved the Doctor by turning him into the Red Mist, so unless it has unlimited uses; I would imagine the Crystal is gone now.
[On the off chance, that the crystal comes back to life after the Doctor and Sue are defeated, then... Well...]
On Ballos and the Red Flowers (Crystal). Many old theories exist on this, and how they are probably connected to Ballos. Also, many theories about how the Core/Ballos make the island float or fall. Use the quicklist or beg me for a lot of links ><
I think that Ballos was sealed by Jenka in that Sealed Chamber, and in that chamber are all the dead skulls and bodies of Ballos' victims. Jenka probably put them there, and they probably act as some kind of seal; the dead trying to drag Ballos to hell or something for destroying a kingdom worth of people, but since Ballos' wild magic is so powerful even the dead cannot take Ballos even if he wants to die himself. In the end though, when Quote weakens Ballos the dead seem to close in and maybe finally take Ballos. "So hot, the pain..." etc (That or Ballos or The Doctor will live yet again!)
Anyways, although Ballos is sealed; his wild magic seems to be able to leak out. The Demon Crown for instance, is probably a good example of this. It will return again even if destroyed, and again as long as Ballos lives. This probably means there is some link to Ballos' direct energy. (Unless it's like how a curse works, as long as the curser lives, it keeps happening?)
The Red Flowers, the Core and how the island floats.
What are the Red Flower's power? Gain wild strength and power at the loss of control. Sound familiar? Ballos let his magic run wild and became invincible, but he lost control of that power and cannot even die if he wants to...
I would think the Red Flowers are connected to Ballos indirectly somehow. Maybe Ballos' wild magic can leak out of the Seal Chamber like radiation.
If the island is under constant threat of Ballos' radiation, shouldn't the island be completely infested and wild? Well, no; not exactly. The Core.
The Core is said to make the island float. It starts falling when destroyed as well. But, the island stops falling when Ballos is destroyed; and Curly says it might be because of the wild/negative energy of Ballos.
I think the radiation is absorbed or fed upon by the Core. It is able to naturally stop Ballos' energy from wreaking havoc on the island. When the big Core is destroyed the energy is free to shake the island and send it plummeting to the ground. It probably would become like a virus and spread into the earth if it were to crash...
On the island's floating and the Core...
Does it make the island actually float? Or is there something else? (If you take Booster, Kazuma, Misery's word for it literally, then yes. And perhaps the little cores that circle around the Big Core allow the island to float; but without the Big Core, Ballos' power is too strong and is sending the island crashing down...)
Back to the Red Flowers and their transformation.
When the Core is destroyed, Kazuma says that any Frenzied Mimigas affected by the Red Flower will return to normal. Perhaps, Ballos' energy leaks out of the Seal Chamber in raw form, but then the Core absorbs and changes this energy into something it can use.
Now is the Core the Heart of the island, and Ballos' energy the Blood that runs through it? If so, perhaps the island is connected to the Core and is sometimes infected by that wild energy, even though it should be rendered harmless by the Core. (Maybe the Demon Crown has something to do with that?)
Alternatively, the Flowers could be a creation of Jenka; if you believe she created the Core, then perhaps the Flowers also had some kind of purpose?
Connected to the Core because, the effects of the Red Flower disappear upon the Core's destruction.
NOW BACK TO THE RED CRYSTAL!
If Red Crystal is Red Flower refined, then the Crystal is probably rendered useless with the Core's destruction.
If Ballos -> wild magic -> Core -> processed magic -> Red Flowers -> Red Crystal
Then, in the best ending there is almost no hope that the crystal is intact with its power. (Still, there could be a chance that by crystalizing it, it acts independently...)
Lastly, on the Doctor and the Demon Crown.
Both, The Doctor and Ballos seem to live even after being destroyed. Assuming everything about Ballos, the wild magic and the flowers and core is true. Then like the Demon Crown, which is reborn everytime it is destroyed. And how Ballos cannot die, and even when destroyed might have been speaking "So hot... the pain...". The Doctor might still be alive, until Ballos is destroyed. However, IF there is a magical connection to the Core. If the red flower transformation disappears when the core is destroyed and the crystal is connected as well... Then I would imagine, the power of the transformations/the Doctor Red Mist himself would return to the source of the power... aka Ballos.
You could argue that at the very end, the is Doctor speaking, "So hot... the pain..." And in that case perhaps he is finally dying. OR PERHAPS THE DOCTOR IS NOW INHERITING BALLOS' WILD MAGIC (with Ballos' demise)! The Doctor will lose his sanity and gain Ballos' curse, but a terrible power might be born... Perhaps his bodiless form can even leave the Seal Chamber?
That, or he is dragged to hell along with Ballos in the end.