LAFORGE: Captain, we've found a way to extend the matter-antimatter energy supplies.
I think going back to "Mirror,Mirror" and "The Alternative Factor" this is why these crystals are so sought after. Apply matter-antimatter energy to it and they give you back matter-antimatter fuel to use again!
That's not how I read this dialogue. Geordi has merely found a way to make more efficient
use of the available matter and antimatter supplies, thus allowing to make extended use of what's available.
I think there is a high probability that "drained" or "discharged" crystals are merely colloquialisms. To an ordinary person it may seem that the crystals' high output is because of a discharge while in fact it's merely the amplification of energy channeled into the crystal (though that would tell us a lot about the amplifying capabilities of these crystals. Wow!
Where we are not looking at a colloquialism is "antimatter". There's a clear distinction bewtween matter, antimatter, dark matter and negative matter (and where it's not, it's probably just bad scriptwriting