I'm guessing you've been playing Flare X on Android, which is by a different developer. They don't really share back their changes, but fighting that is pretty much impossible. So we just do our thing and let them do their's.
The data for gem items is still around from when the "alpha demo" was the primary game packaged with the engine. Back then, the gems only served as an alternative to gold, so I didn't bother carrying them over to the Empyrean Campaign. Well, there are a few quest items that are gems, but none outside of that.
I'd be willing to bring the gems back so they don't go unused, but maybe give them a secondary purpose. Crafting seems like a good application.