You completely missed transmuting them with alchemy.
If Alchemy is the only source of epic gems, there's only 2 possible scenarios once the patch hits.
1) There's a cooldown on the transmute, and prices are ABSURD. Gems are much much much more scarce than any gem in the history of the game. They would never do this, because it's retarded.
2) There's no cooldown on the transmute, and prices are rock bottom. Gems are so common you can hardly give them away, much like rare gems are now. They would never do this, because it's retarded.
I fully expect Pyrite and JP/HP to be the sources for gems, and probably an alchemy transmute with a 20hr cooldown as we've seen previously.