IIRC, my idea about the crystals was that they:
1. regenerated antimatter (and matter fuel) when m/am energy is applied to them by possibly borrowing from an antimatter universe
2. they store a charge like a giant capacitor or battery
I remember from your thread several TOS quotes that do hint the ship's capability to "re-energize" itself, i.e. refuel antimatter but I find your antimatter universe idea to be too "exotic" - for my taste that is.
My understanding of crystals is limited but from what I've read they act as amplifiers (Kirk: "re-amplify"!) and oscillators. Thus, the output is bigger than the input and if I'm not totally mistaken you can use the extra output to generate new antimatter from ordinary matter (plenty available via the Bussard "sinks" and thanks to warped space). I'm aware it's equally exotic but I believe this to be within established treknological parameters.
I believe this charge storage idea to come from "The Alternative Factor" but having just seen the episode - again - (is this "Cause and Effect"?
) I can't help the feeling that it is rather the incredible amount of charges that is channeled through these (diminishing their capabilities, hence the necessity to regenerate, re-amplify or re-energize these) than an actual discharge of the crystals that's weakening their power (i.e. capability).
Let's also not forget that the screenplay is in some parts pure rubbish: Kirk arrives on a planet vis-a-vis the "good" Lazarus who consists of antimatter. This meeting couldn't
take place, neither in our matter universe nor a hypothetical animatter universe.
We should take treknological conclusions from this episode with appropriate quantities of salt, IMHO.